3,3'-Neotrehalosadiamine (BMY-28251), a new aminosugar antibiotic

Impact of activation of neotrehalosadiamine/kanosamine biosynthetic pathway on the metabolism of Bacillus subtilis

The pentose phosphate (PP) pathway is one of the major sources of cellular NADPH. A B. subtilis zwf mutant that lacks glucose-6-phosphate dehydrogenase (the enzyme that catalyzes the first step of the PP pathway) showed inoculum-dose-dependent growth. This growth defect was suppressed by glcP disruption, which causes the upregulation of an autoinducer neotrehalosadiamine (NTD)/kanosamine biosynthetic pathway. A metabolome analysis showed that the stimulation of NTD/kanosamine biosynthesis caused significant accumulation of TCA cycle intermediates and NADPH. Because the major malic enzyme YtsJ concomitantly generates NADPH through malate-to-pyruvate conversion, de novo NTD/kanosamine biosynthesis can result in an increase in the intracellular NADPH pool via the accumulation of malate. In fact, a zwf mutant grew in malate-supplemented medium. Artificial induction of glcP in the zwf mutant caused a reduction in the intracellular NADPH pool. Moreover, the correlation between the expression level of the NTD/kanosamine biosynthesis operon ntdABC and the intracellular NADPH pool was confirmed. Our results suggest that NTD/kanosamine has the potential to modulate the carbon-energy metabolism through an autoinduction mechanism.ImportanceAutoinducers enable bacteria to sense cell density and to coordinate collective behavior. NTD/kanosamine is an autoinducer produced by B. subtilis and several close relatives, although its physiological function remains unknown. The most important finding of this study was the significance of de novo NTD/kanosamine biosynthesis in the modulation of the central carbon metabolism in B. subtilis We showed that NTD/kanosamine biosynthesis caused an increase in the NADPH pool via the accumulation of TCA cycle intermediates. These results suggest a possible role for NTD/kanosamine in the carbon-energy metabolism. As Bacillus species are widely used for the industrial production of various useful enzymes and compounds, the NTD/kanosamine biosynthetic pathway might be utilized to control metabolic pathways in these industrial strains.

Bioactive Secondary Metabolites from Bacillus subtilis: A Comprehensive Review

Bacillus subtilis is widely underappreciated for its inherent biosynthetic potential. This report comprehensively summarizes the known bioactive secondary metabolites from B. subtilis and highlights potential applications as plant pathogen control agents, drugs, and biosurfactants. B. subtilis is well known for the production of cyclic lipopeptides exhibiting strong surfactant and antimicrobial activities, such as surfactins, iturins, and fengycins. Several polyketide-derived macrolides as well as nonribosomal peptides, dihydroisocoumarins, and linear lipopeptides with antimicrobial properties have been reported, demonstrating the biosynthetic arsenal of this bacterium. Promising efforts toward the application of B. subtilis strains and their natural products in areas of agriculture and medicine are underway. However, industrial-scale availability of these compounds is currently limited by low fermentation yields and challenging accessibility via synthesis, necessitating the development of genetically engineered strains and optimized cultivation processes. We hope that this review will attract renewed interest in this often-overlooked bacterium and its impressive biosynthetic skill set.

Diverse Synthesis of Natural Trehalosamines and Synthetic 1,1'-Disaccharide Aminoglycosides

A general strategy for the diverse synthesis of ten disaccharide aminoglycosides, including natural 2-trehalosamine (1), 3-trehalosamine (2), 4-trehalosamine (3), and neotrehalosyl 3,3'-diamine (8) and synthetic aminoglycosides 4-7, 9, and 10, has been developed. The aminoglycoside compounds feature different anomeric configurations and numbers of amino groups. The key step for the synthesis was the glycosylation coupling of a stereodirecting donor with a configuration-stable TMS glycoside acceptor. Either the donor or acceptor could be substituted with an azido group. The aminoglycosides prepared in the present study were characterized by 1D and 2D NMR spectroscopy.

Unusually Stable Picoloyl-Protected Trimethylsilyl Glycosides for Nonsymmetrical 1,1'-Glycosylation and Synthesis of 1,1'-Disaccharides with Diverse Configurations

Nonsymmetrical 1,1'-disaccharides and related derivatives constitute structural components in various glycolipids and natural products. Some of these compounds have been shown to exhibit appealing biological properties. We report a direct yet stereoselective 1,1'-glycosylation strategy for the synthesis of nonsymmetrical 1,1'-disaccharides with diverse configurations and sugar components. The strategy is based on the joined forces of a new class of configurationally stable glycoside acceptors and stereodirecting thioglycoside donors. The new glycoside acceptors feature a picoloyl (Pico) protecting group at the remote C4/C3 position that confers unusual stability on TMS glycosides under acidic conditions.

The mthA mutation conferring low-level resistance to streptomycin enhances antibiotic production in Bacillus subtilis by increasing the S-adenosylmethionine pool size

Certain Str(r) mutations that confer low-level streptomycin resistance result in the overproduction of antibiotics by Bacillus subtilis. Using comparative genome-sequencing analysis, we successfully identified this novel mutation in B. subtilis as being located in the mthA gene, which encodes S-adenosylhomocysteine/methylthioadenosine nucleosidase, an enzyme involved in the S-adenosylmethionine (SAM)-recycling pathways. Transformation experiments showed that this mthA mutation was responsible for the acquisition of low-level streptomycin resistance and overproduction of bacilysin. The mthA mutant had an elevated level of intracellular SAM, apparently acquired by arresting SAM-recycling pathways. This increase in the SAM level was directly responsible for bacilysin overproduction, as confirmed by forced expression of the metK gene encoding SAM synthetase. The mthA mutation fully exerted its effect on antibiotic overproduction in the genetic background of rel(+) but not the rel mutant, as demonstrated using an mthA relA double mutant. Strikingly, the mthA mutation activated, at the transcription level, even the dormant ability to produce another antibiotic, neotrehalosadiamine, at concentrations of 150 to 200 μg/ml, an antibiotic not produced (<1 μg/ml) by the wild-type strain. These findings establish the significance of SAM in initiating bacterial secondary metabolism. They also suggest a feasible methodology to enhance or activate antibiotic production, by introducing either the rsmG mutation to Streptomyces or the mthA mutation to eubacteria, since many eubacteria have mthA homologues.

The structure of NtdA, a sugar aminotransferase involved in the kanosamine biosynthetic pathway in Bacillus subtilis, reveals a new subclass of aminotransferases

NtdA from Bacillus subtilis is a sugar aminotransferase that catalyzes the pyridoxal phosphate-dependent equatorial transamination of 3-oxo-α-D-glucose 6-phosphate to form α-D-kanosamine 6-phosphate. The crystal structure of NtdA shows that NtdA shares the common aspartate aminotransferase fold (Type 1) with residues from both monomers forming the active site. The crystal structures of NtdA alone, co-crystallized with the product α-D-kanosamine 6-phosphate, and incubated with the amine donor glutamate reveal three key structures in the mechanistic pathway of NtdA. The structure of NtdA alone reveals the internal aldimine form of NtdA with the cofactor pyridoxal phosphate covalently attached to Lys-247. The addition of glutamate results in formation of pyridoxamine phosphate. Co-crystallization with kanosamine 6-phosphate results in the formation of the external aldimine. Only α-D-kanosamine 6-phosphate is observed in the active site of NtdA, not the β-anomer. A comparison of the structure and sequence of NtdA with other sugar aminotransferases enables us to propose that the VIβ family of aminotransferases should be divided into subfamilies based on the catalytic lysine motif.

A previously unrecognized kanosamine biosynthesis pathway in Bacillus subtilis

The ntd operon in Bacillus subtilis is essential for biosynthesis of 3,3'-neotrehalosadiamine (NTD), an unusual nonreducing disaccharide reported to have antibiotic properties. It has been proposed that the three enzymes encoded within this operon, NtdA, NtdB, and NtdC, constitute a complete set of enzymes required for NTD synthesis, although their functions have never been demonstrated in vitro. We now report that these enzymes catalyze the biosynthesis of kanosamine from glucose-6-phosphate: NtdC is a glucose-6-phosphate 3-dehydrogenase, NtdA is a pyridoxal phosphate-dependent 3-oxo-glucose-6-phosphate:glutamate aminotransferase, and NtdB is a kanosamine-6-phosphate phosphatase. None of these enzymatic reactions have been reported before. This pathway represents an alternate route to the previously reported pathway from Amycolatopsis mediterranei which derives kanosamine from UDP-glucose.

Secondary metabolites of soil Bacillus spp

Bacillus species produce secondary metabolites that are the object of natural product chemistry studies. The wide structural variability of these compounds has attracted the curiosity of chemists and their biological activities have inspired the pharmaceutical industry to search for lead structures in microbial extracts. Screening of microbial extracts reveals the large structural diversity of natural compounds with broad biological activities, such as antimicrobial, antiviral, immunosuppressive, and antitumor activities, that enable the bacterium to survive in its natural environment. These findings widen the potential industrial importance of Bacillus spp., particularly of B. thuringiensis, beyond insecticidal usage and may help explain the role of Bacillus spp. in the soil ecosystem.

Non-peptide metabolites from the genus Bacillus

Bacillus species produce a number of non-peptide metabolites that display a broad spectrum of activity and structurally diverse bioactive chemical structures. Biosynthetic, biological, and structural studies of these metabolites isolated from Bacillus species are reviewed. This contribution also includes a detailed study of the activity of the metabolites described, especially their role in biological control mechanisms.

Activation of dormant secondary metabolism neotrehalosadiamine synthesis by an RNA polymerase mutation in Bacillus subtilis

Microorganisms possess the ability to produce a variety of commercially important secondary metabolites such as antibiotics. Although it becomes harder and harder to discover useful new compounds, microorganisms still have the potential to produce unknown compounds. One of the reasons for the difficulty in finding new compounds is that the expression level of many secondary metabolite genes is insufficient in wild-type strains. Therefore, a new method of activating gene expression might be a powerful tool for the screening of novel compounds and for strain improvement to overproduce useful compounds. We found that the rifampicin-resistant RNA polymerase mutations stimulate the expression of antibiotic synthetic gene clusters in several microorganisms. In the case of the Gram-positive model organism Bacillus subtilis, one of the rifampicin-resistance mutations resulted in the activation of a dormant secondary metabolism, neotrehalosadiamine synthesis. To clarify this activation mechanism, we first identified the neotrehalosadiamine biosynthetic operon and investigated its transcriptional regulation. Here we summarize our findings on the transcriptional regulation of the neotrehalosadiamine biosynthetic operon and discuss a crucial effect of the rifampicin-resistance mutation on the expression of dormant genes.

Purification, crystallization and preliminary X-ray analysis of NtdA, a putative pyridoxal phosphate-dependent aminotransferase from Bacillus subtilis

NtdA is a putative sugar aminotransferase that is required for the synthesis of 3,3'-neotrehalosadiamine. The enzyme was purified to homogeneity by means of Ni(2+)-affinity chromatography and was crystallized using the microbatch method. X-ray diffraction data were collected from a single crystal to 2.3 A resolution at the Canadian Light Source (CLS). The crystals belonged to space group P2(1), with unit-cell parameters a = 50.3, b = 106.7, c = 96.7 A, beta = 96.2 degrees, and contained two molecules per asymmetric unit.

Glucose uptake pathway-specific regulation of synthesis of neotrehalosadiamine, a novel autoinducer produced in Bacillus subtilis

Neotrehalosadiamine (3,3'-diamino-3,3'-dideoxy-alpha,beta-trehalose; NTD) is an amino-sugar antibiotic produced by several Bacillus species that functions as an autoinducer by activating its own biosynthetic operon, ntdABC. We previously reported that the introduction of a certain rpoB mutation (rpoB5) into Bacillus subtilis enables the cells to overproduce NTD. B. subtilis mini-Tn10 transposant libraries have been screened for genes that affect NTD production. Inactivation of ccpA, which encodes a major transcriptional regulator of carbon catabolite regulation, markedly reduced NTD production. By contrast, inactivation of glcP, which is situated just downstream of ntdABC and encodes a glucose/mannose:H(+) symport permease, stimulated NTD production. Overexpression of glcP led to the repression of ntdABC expression (and thus NTD production) in response to GlcP-mediated glucose uptake. These results suggest that CcpA-mediated catabolite activation of ntdABC expression occurs in response to the increase of the in vivo concentration of fructose-1,6-bisphosphate via glucose-6-phosphate and that GlcP-mediated glucose repression of ntdABC expression occurs in association with the increase of the in vivo concentration of unphosphorylated glucose. In addition, Northern analysis showed that glcP is transcribed from the ntdABC promoter through transcription readthrough at the ntdABC transcription terminator site, which enables NTD to function as a modulator of glucose uptake through the stimulation of ntdABC-glcP transcription, even in wild-type (rpoB(+)) cells. A trace amount (0.5 to 3 mug/ml) of NTD was sufficient to ensure expression of glcP, thus demonstrating the physiological role of "antibiotic" in the producing bacteria by functioning as an autoinducer for glucose uptake modulation.

RNA polymerase mutation activates the production of a dormant antibiotic 3,3'-neotrehalosadiamine via an autoinduction mechanism in Bacillus subtilis

Bacillus and Streptomyces species possess the ability to produce a variety of commercially important metabolites and extracellular enzymes. We previously demonstrated that antibiotic production in Streptomyces coeli-color A3(2) and Streptomyces lividans can be enhanced by RNA polymerase (RNAP) mutations selected for the rifampicin-resistant (Rif(r)) phenotype. Here, we have shown that the introduction of a certain Rif(r) rpoB mutation into a B. subtilis strain resulted in cells that overproduce an aminosugar antibiotic 3,3'-neotrehalosadiamine (NTD), the production of which is dormant in the wild-type strain. Mutational and recombinant gene expression analyses have revealed a polycistronic gene ntdABC (formally yhjLKJ) and a monocistronic gene ntdR (formally yhjM) as the NTD biosynthesis operon and a positive regulator for ntdABC, respectively. Analysis of transcriptional fusions to a lacZ reporter revealed that NTD acts as an autoinducer for its own biosynthesis genes via NtdR protein. Our results also showed that the Rif(r) rpoB mutation causes an increase in the activity of sigma(A)-dependent promoters including ntdABC promoter. Therefore, we propose that unlike the wild-type RNAP, the mutant RNAP efficiently recognized the sigma(A)-dependent promoters, resulting in the dramatic activation of the NTD biosynthesis pathway by an autoinduction mechanism.

Guanine nucleotides guanosine 5'-diphosphate 3'-diphosphate and GTP co-operatively regulate the production of an antibiotic bacilysin in Bacillus subtilis

We found that a polycistronic operon (ywfBCDEFG) and a monocistronic gene (ywfH) are required for the biosynthesis of bacilysin in Bacillus subtilis. The disruption of these genes by plasmid integration caused loss of the ability to produce bacilysin, accompanied by a lack of bacilysin synthetase activity in the crude extract. We investigated the regulatory mechanism for bacilysin biosynthesis using the transcriptional lacZ fusion system. The transcription of these genes was found to be induced at the transition from exponential to stationary phase. Induction of transcription was accelerated by depleting a required amino acid, which was done by transferring the wild-type (rel(+)) cells to an amino acid-limited medium. In contrast, no enhancement of the gene expression was detected in relA mutant cells. In wild-type (rel(+)) cells, a forced reduction of intracellular GTP, brought about by addition of decoyinine, which is a GMP synthetase inhibitor, enhanced the expression of both the ywfBCDEFG operon and the ywfH gene, resulting in a 2.5-fold increase in bacilysin production. Disruption of the codY gene, which regulates stationary phase genes by detecting the level of GTP, also induced transcription of these genes. In contrast, the expression of ywfBCDEFG in relA cells was not activated either by decoyinine addition or codY disruption, although the expression of ywfH was induced. Moreover, the codY disruption resulted in an increase of bacilysin production only in rel(+) cells. These results indicate that guanosine 5'-diphosphate 3'-diphosphate (ppGpp) plays a crucial role in transcription of the ywfBCDEFG operon and that the transcription of these genes are dependent upon the level of intracellular GTP which is transmitted as a signal via the CodY-mediated repression system. We propose that, unlike antibiotic production in Streptomyces spp., bacilysin production in B. subtilis is controlled by a dual regulation system composed of the guanine nucleotides ppGpp and GTP.

Kanosamine biosynthesis: a likely source of the aminoshikimate pathway's nitrogen atom

The biosynthetic source of the nitrogen atom incorporated into the aminoshikimate pathway has remained a question for some time. 3-Amino-3-deoxy-D-fructose 6-phosphate has previously been demonstrated to be a precursor to 4-amino-3,4-dideoxy-D-arabino-heptulosonic acid 7-phosphate and 3-amino-5-hydroxybenzoic acid via the inferred intermediacy of 1-deoxy-1-imino-D-erythrose 4-phosphate in Amycolatopsis mediterranei cell-free extract. This investigation examines the possibility that the natural product kanosamine might be a precursor to 3-amino-3-deoxy-D-fructose 6-phosphate. Kanosamine 6-phosphate was synthesized by a chemoenzymatic route and incubated in A. mediterranei cell-free lysate along with D-ribose 5-phosphate and phosphoenolpyruvate. Formation of 4-amino-3,4-dideoxy-D-arabino-heptulosonic acid 7-phosphate and 3-amino-5-hydroxybenzoic acid was observed. Subsequent incubation in A. mediterranei cell-free lysate of glutamine and NAD with UDP-glucose resulted in the formation of kanosamine. The bioconversion of UDP-glucose into kanosamine along with the bioconversion of kanosamine 6-phosphate into 4-amino-3,4-dideoxy-D-arabino-heptulosonic acid 7-phosphate and 3-amino-5-hydroxybenzoic acid suggests that kanosamine biosynthesis is the source of the aminoshikimate pathway's nitrogen atom.

Highly stereoselective synthesis of alpha,beta-linked, nonreducing disaccharides related to tunicamycin

3,4,6-Tri-O-benzoyl-2-(benzoyloxyimino)-2-deoxy-alpha-D-arabino-++ +hexopyranosy l bromide (2) reacts with the O-protected 2-deoxy-2-phthalimido-beta-D-galactosamines 3 and 4 in the presence of silver triflate and sym-collidine at -78 degrees C, to give alpha,beta-(1-->1)-linked disaccharides 6a and 7a with an excellent selectivity. The 2-oxyimino function was stereospecifically converted into a 2-acetamido group by use of the LiBH4-Me3SiCl-THF reductive species, furnishing, after acetylation, the alpha-D-GlcNAc-(1-->1)-beta-D-GalNPhth nonsymmetrical, trehalose type disaccharides 13 and 14 related to tunicamycin (1, part A). Similarly, alpha-D-GlcNAc-(1-->1)-beta-D-GlcNPhth (15) was prepared, starting from 2 and 5. The factors governing the stereoselectivity of the glycosylation reactions were determined.

Mechanism-based screens in the discovery of chemotherapeutic antibacterials

Numerous assays have been developed over the last 40 years for the detection of novel antibacterial metabolites. I have discussed many of the successful strategies and suggested some potential targets. Although the trend toward mechanism-based assays is relatively recent, it is clear that they have had a profound impact on screening in drug discovery. Often a mechanism-based assay requires construction of specific strains and verification of the antibacterial role of the selected target. Since the conception and development of a mechanism-based screen depends upon knowledge of the specific target and perhaps a compound that affects that target, it is implicit that mode of action studies on compounds discovered through random screening may subsequently lead to new mechanistic assays. While serendipity continues to play a crucial role in any screen, target-directed assays appear to be a worthwhile approach in antibacterial screening.

Detection of novel secondary metabolites

The study of antibiotics and other fermentation products has shown that a seemingly unlimited number of compounds with diverse structures are produced by microorganisms. The continued high rate of discovery of new chemical entities, in the light of the abundance of microbial products already described, is due to creative screening procedures that incorporate such features as the emphasis on unusual microorgnaisms, their special propagation and fermentation requirements, supersensitive and highly selective assays, genetic engineering both for the biosynthesis of new compounds and in the development of screening systems, early in vivo evaluation, improved isolation techniques, modern procedures for structure determination, computer-assisted identification, and an efficient multidisciplinary approach. This review focuses on the genesis and development of the gamut of methodologies that have led to the successful detection of the wide variety of novel secondary metabolites that include antibacterial, antigungal, antiviral and antitumour antibiotics, enzyme inhibitors, pharmacologically and immunologically active agents, products useful in agriculture and animal husbandry, microbial regulators, and other compounds for which no bioactive role has yet been found.