Existence of two alternative pathways for fructose and sorbitol metabolism in Bacillus subtilis Marburg

Essential bacterial functions encoded by gene pairs

To address the need for new antibacterials, a number of bacterial genomes have been systematically disrupted to identify essential genes. Such programs have focused on the disruption of single genes and may have missed functions encoded by gene pairs or multiple genes. In this work, we hypothesized that we could predict the identity of pairs of proteins within one organism that have the same function. We identified 135 putative protein pairs in Bacillus subtilis and attempted to disrupt the genes forming these, singly and then in pairs. The single gene disruptions revealed new genes that could not be disrupted individually and other genes required for growth in minimal medium or for sporulation. The pairwise disruptions revealed seven pairs of proteins that are likely to have the same function, as the presence of one protein can compensate for the absence of the other. Six of these pairs are essential for bacterial viability and in four cases show a pattern of species conservation appropriate for potential antibacterial development. This work highlights the importance of combinatorial studies in understanding gene duplication and identifying functional redundancy.

Roles of glucitol in the GutR-mediated transcription activation process in Bacillus subtilis: glucitol induces GutR to change its conformation and to bind ATP

GutR is a 95-kDa glucitol-dependent transcription activator that mediates the expression of the Bacillus subtilis glucitol operon. Glucitol allows GutR to bind tightly to its binding site located upstream of the gut promoter. In this study, a second functional role of glucitol is identified. Glucitol induces GutR to change its conformation and triggers GutR to bind ATP efficiently. After sequential binding of glucitol and ATP to GutR, GutR adopts a new conformation by forming a compact structure that is resistant to trypsin digestion. Under this condition, the ATP.glucitiol.GutR complex can dissociate slowly from the gutR-binding site (t(12) = 274 min). Interestingly, if ATP in the ATP.glucitiol.GutR complex is replaced by ADP, GutR adopts another conformation and can dissociate from the gutR-binding site even faster (t(12) = 82 min). In all these GutR-DNA binding studies in the presence of different ligands (glucitol, ATP, or ADP), only the off-rate is affected. The vital role of ATP in the GutR-mediated transcription activation process is reflected by the poor transcription from the gut promoter with GutR(D285A) which has a mutation in the motif B of the putative ATP-binding site. A working model for this transcription activation process is presented.

Initial catabolism of sorbitol in Actinomyces naeslundii and Actinomyces viscosus

The initial steps of sorbitol catabolism were studied in 4 strains of Actinomyces naeslundii and Actinomyces viscosus that had been isolated from human dental plaque. Cell-free extracts were prepared from cells grown in the presence of either sorbitol, xylitol or glucose. The extracts from all strains grown on sorbitol had nicotinamide adenine dinucleotide-linked dehydrogenase activities for sorbitol and xylitol and reduced nicotinamide adenine dinucleotide-linked reductase activities for fructose and xylulose. Two of the strains also exhibited these activities when grown in the presence of xylitol, and all glucose-grown cells lacked them. The results indicate that sorbitol metabolism in oral actinomyces involve oxidation of sorbitol to fructose by an inducible enzyme, nicotinamide adenine dinucleotide-linked sorbitol dehydrogenase. This step is followed by the phosphorylation of fructose with guanosine triphosphate as a main phosphoryl donor. Thus, the initial catabolic pathway of sorbitol in A. naeslundii and A. viscosus is different from those described for other oral bacteria.

Transcriptional regulation of the Bacillus subtilis glucitol dehydrogenase gene

The regulatory region of the Bacillus subtilis glucitol dehydrogenase (gutB) gene was divided into three subregions: a promoter, an upstream positive regulatory region, and a downstream negative regulatory region. Data from primer extension, deletion, and site-directed mutagenesis analyses were consistent with two possible models for the gutB promoter. It is either a sigma A-type promoter with an unusually short spacer region (15 bp) or a special sigma A promoter which requires only the hexameric -10 sequence for its function. Sequence carrying just the promoter region (from -48 to +6) failed to direct transcription in vivo. An upstream regulatory sequence was essential for glucitol induction. When this sequence was inserted in a high-copy-number plasmid, an effect characteristic of titration of a transcriptional activator was seen. Downstream from the promoter, there is an imperfect, AT-rich inverted repeat sequence. Deletion of this element did not lead to constitutive expression of gutB. However, the induced gutB expression level was enhanced three- to fourfold.

Purification and properties of sorbitol-6-phosphate dehydrogenase from oral streptococci

The activity of sorbitol-6-phosphate (S6P) dehydrogenase (S6PDH) and the sorbitol transport system were studied in strains of the oral streptococci Streptococcus gordonii, Streptococcus mitis, Streptococcus sanguis and Streptococcus mutans. Genetically transformed (to ferment sorbitol) strains and their DNA donors were included. S6PDH was purified by anion exchange chromatography and gel filtration. The purity of the enzyme was confirmed by polyacrylamide gel electrophoresis. The purified enzyme from all the strains exhibited Michaelis-Menton saturation kinetics. The Km values for nicotinamide-adenine dinucleotide (NAD) and S6P ranged between 0.03 and 0.21 mM and 0.07 and 0.20 mM respectively. The relative molecular weights of the native enzyme were 229,000 for one donor-transformant pair (S. sanguis and S. gordonii), 107,000 for the other pair (S. mitis and S. gordonii) and 129,000 for S. mutans. The molecular weights of the S6PDH subunits ranged from 26,000 to 28,000. The pH optima (greater than 8.5) and the amino acid composition (15 amino acids examined) were similar for the S6PDH from the different strains. However, the chromatographic and electrophoretic patterns as well as the Km values for NAD and S6P were the same only between the S6PDHs from the strains within each donor-transformant pair. Purified S6PDH from S. mutans also exhibited low mannitol-1-phosphate dehydrogenase activity. Sorbitol-grown decryptified cells of all the strains phosphorylated sorbitol in the presence of phosphoenolpyruvate but not in the presence of adenosine triphosphate (ATP). ATP-mediated phosphorylation of glucose was observed with the same strains when grown on glucose. No evidence for a non-phosphotransferase transport system was found for sorbitol in any of the strains.(ABSTRACT TRUNCATED AT 250 WORDS)

Kinetic study of a phosphoryl exchange reaction between fructose and fructose 1-phosphate catalyzed by the membrane-bound enzyme II of the phosphoenolpyruvate-fructose 1-phosphotransferase system of Bacillus subtilis

A phosphoryl exchange reaction between fructose 1-phosphate and fructose was found to be catalyzed by a membrane preparation isolated from Bacillus subtilis. The regulation of the biosynthesis of the activity in the wild type as well as in the regulation mutants fruB closely correlates with that of the membrane-bound enzyme II of the phosphoenolpyruvate fructose 1-phosphotransferase system which is known to mediate the transmembrane vectorial phosphorylation of fructose. The computed analysis of the kinetic data shows that the mechanism of the enzyme II is ping-pong, i.e. that a phosphoryl-enzyme intermediate occurs in the reaction. The apparent dissociation constants of the enzyme II/fructose 1-phosphate complex and of the phosphoryl enzyme II/fructose complex are estimated. The value of the standard free energy of the hydrolysis of the bond between the phosphoryl moiety and the enzyme suggests a covalent bonding. This intermediate is assumed to occur in the physiological functioning of the enzyme which utilizes the phosphocarrier protein HPr as phosphoryl donor. The exchange reaction is competitively inhibited by high fructose concentrations: this indicates that the same site of the enzyme binds fructose and fructose 1-phosphate, this site being accessible to fructose on the external side of the membrane when the enzyme is phosphorylated.

Biochemical and genetic study of D-glucitol transport and catabolism in Bacillus subtilis

The catabolic pathway of D-glucitol (sorbitol) in Bacillus subtilis Marburg 168M is characterized. It includes (i) a transport step catalyzed by a D-glucitol permease which is affected by the gutA mutations, (ii) an oxidation step of the intracellular D-glucitol catalyzed by a D-glucitol dehydrogenase, generating intracellular fructose, affected by gutB mutations, and (iii) phosphorylation of the intracellular fructose either at the C1 site or at the C6 site as described previously (A. Delobbe et al., Eur. J. Biochem., 66:485-491, 1976; A. Delobbe et al., EUR. J. Biochem. 51:503-510, 1975). Additional data are given concerning the phosphorylation of fructose by a fructokinase (fructose ATP 6-phosphotransferase), which is affected by the fruC mutation. The isolation of regulatory mutants affected in gutR that synthesize constitutively both the permease and the dehydrogenase indicates the existence of a D-glucitol operon in B. subtilis. Unlike the wild-type strain, these mutants are able to utilize D-xylitol as sole carbon source.

Fructose transport in Bacillus subtilis

The transport of fructose in Bacillus subtilis was studied in various mutant strains lacking the following activities: ATP-dependent fructokinase (fruC), the fructose 1-phosphate kinase (fruB) the phosphofructokinase (pfk), the enzyme I of the phosphoenolpyruvate phosphotransferase system (the thermosensitive mutation ptsI1), and a transport activity (fruA). Combinations of these mutations indicated that the transport of fructose in Bacillus subtilis is tightly coupled to its phosphorylation either in fructose 1-phosphate, identified in vivo and in vitro or in fructose 6-phosphate identified by indirect lines of evidence. These steps of fructose metabolism were shown to depend on the activity of the enzyme I of the phosphoenolpyruvate phosphotransferase systems. The fruA mutations affect the transport of fructose when the bacteria are submitted to catabolite repression. The mutations were localized on the chromosome of Bacillus subtilis in a cluster including the fruB gene. When grown in a medium supplemented by a mixture of potassium glutamate and succinate the fruA mutants are able to carry on the two vectorial metabolisms generating fructose 6-phosphate as well as fructose 1-phosphate. A negative search of strictly negative transport mutants in fruA strains indicated that more than two structural genes are involved in the transport of fructose.

Role of sugar uptake and metabolic intermediates on catabolite repression in Bacillus subtilis

Many phosphorylated intermediates exert catabolite repression on the enzyme acetoin dehydrogenase in Bacillus subtilis. This was shown with strains that are blocked at different positions in central metabolism when they receive sugars that cannot be metabolized past enzymatic block(s). In the case of sorbitol, transport events were not involved in catabolite repression, for this sugar cannot repress acetoin dehydrogenase in a strain lacking sorbitol dehydrogenase but otherwise able to take up sorbitol. The presence of glucose did not markedly influence the uptake of acetoin.

Phosphorylation of intracellular fructose in Bacillus subtilis mediated by phosphoenolpyruvate-1-fructose phosphotransferase

Intracellular fructose provided by the sorbitol pathway in Bacillus subtilis can be phosphorylated by the phosphenolpyruvate-1-fructose phosphotransferase which is known to mediate a vectorial metabolism. The fate of this intracellular fructose was studied using mutants lacking either the fructose 1-phosphate pathway or the fructose 6-phosphate pathway. It was shown that the phosphoenolpyruvate-dependent phosphorylation needs a prior exit of the sugar into the medium, this exit being probably catalysed by a transport system. A low affinitiy intracellular phosphenolpyruvate phosphotransferase system was found, which seems to be devoid of a physiological role.