Antimicrobials, drug discovery, and genome mining.

Over the years, antibiotics have provided an effective treatment for a number of microbial diseases. However recently, there has been an increase in resistant microorganisms that have adapted to our current antibiotics. One of the most dangerous pathogens is methicillin-resistant Staphylococcus aureus (MRSA). With the rise in the cases of MRSA and other resistant pathogens such as vancomycin-resistant Staphylococcus aureus, the need for new antibiotics increases every day. Many challenges face the discovery and development of new antibiotics, making it difficult for these new drugs to reach the market, especially since many of the pharmaceutical companies have stopped searching for antibiotics. With the advent of genome sequencing, new antibiotics are being found by the techniques of genome mining, offering hope for the future.

Industrial microbiology.

Industrial microbiology has served humanity since prebiblical times, providing fermented beverages and foods to enhance the quality of life. The antibiotic era featured an explosion in the number of microbial products for medicine, nutrition, industry, and research. Revolutionary developments in molecular genetics are propelling the field into a new growth phase with promise of solutions to major world problems.

New applications of microbial products.

Microbial secondary metabolites are now being used for applications other than as antibacterial, antifungal, and antitumor agents. These applications include use against parasites (coccidia, helminths) and insects as well as for animal and plant growth stimulation, immunosuppression, uterocontraction, and other pharmacological activities. Further applications are possible in various areas of pharmacology and agriculture, a development catalyzed by the use of simple enzyme assays for screening prior to testing in intact animals or in the field.

Enzymatic approach to syntheses of unnatural beta-lactams.

Four enzymes associated with the transformation of the peptide delta-(L-alpha-aminoadipyl)-L-cysteinyl-D-valine (ACV) into the beta-lactam antibiotic desacetylcephalosporin C have been isolated from the prokaryotic organism Streptomyces clavuligerus and immobilized. Appropriate choice of the cofactors allows continuous and quantitative conversion of the peptide into either penicillins or cephalosporins at room temperature. The overall process includes four oxidations, two ring closures, and one epimerization. In contrast, cell-free transformations with the eukaryotic organism Cephalosporium acremonium do not proceed beyond the oxidation level of penicillin. The amino acids of the natural peptide ACV can be altered by chemical means; several of the resulting peptides are converted into novel antibiotics by the enzymes of Streptomyces clavuligerus.

A pure enzyme catalyzing penicillin biosynthesis.

Isopenicillin N synthetase (cyclase) has been purified to homogeneity from Cephalosporium acremonium strain C-10. The enzyme has a molecular weight of 40,000 to 42,000 and yields a single band on sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The enzyme was purified in 10 percent yield by a combination of protamine sulfate and ammonium sulfate precipitations, gel filtration, and ion-exchange high-performance liquid chromatography. The purified enzyme can be stabilized with sucrose and stored at -20 degrees C for several weeks without any loss in activity.

FACS-based isolation of slowly growing cells: double encapsulation of yeast in gel microdrops.

Isolating hyperproducing cells is important in biotechnology, but these cells usually grow slowly and can be overgrown by poorly producing cells. We describe a new method of isolating slowly growing cells from among rapidly growing cells, which has the potential for automation and high throughput (e.g., 100,000 cells/h). A model system is presented consisting of a mixed population of slowly growing mutant and rapidly growing wild-type yeast, which were encapsulated in double agarose gel microdrops (dGMDs); with most dGMDs initially containing single cells. Double encapsulation locates parent cells near dGMD centers, making microcolony measurement more accurate. After a 15-h incubation, fluorescent activated cell sorting was used to analyze and sort dGMDs with small microcolonies (slow growers) from dGMDs with large microcolonies (rapid growers). Successful isolation of slow growers from a mixed population of predominantly rapidly growing Saccharomyces cerevisiae cells was achieved.

Regulation of extracellular protease production in Candida lipolytica.

Production of extracellular protease by Candida lipolytica NRRL Y-1094 was derepressed upon transfer to carbon-, nitrogen- or sulphur-free medium but not upon transfer to phosphorus-free medium. The protease activities produced under the three nutrient limitations had alkaline pH optima and similar substrate and inhibitor specificities. Any one of the following three conditions was found to be sufficient for derepression of extracellular protease: (a) "poor" carbon source, (b) cysteine intracellular pool below 0.5 micronmol/g dry weight cells and (c) ammonia intracellular pool below 10 micronmol/g dry weight cells. Thus, extracellular protease production in C. lipolytica was subject to at least three different regulatory controls, carbon, sulphur and nitrogen repression. Intracellular cysteine and ammonia appeared to be the metabolic signals for sulphur and nitrogen repression, respectively. Anabolic glutamate dehydrogenase did not act as a regulatory protein mediating nitrogen repression. Exogenous protein had an inductive effect on extracellular protease production.

Microbial biotechnology.

For thousands of years, microorganisms have been used to supply products such as bread, beer and wine. A second phase of traditional microbial biotechnology began during World War I and resulted in the development of the acetone-butanol and glycerol fermentations, followed by processes yielding, for example, citric acid, vitamins and antibiotics. In the early 1970s, traditional industrial microbiology was merged with molecular biology to yield more than 40 biopharmaceutical products, such as erythropoietin, human growth hormone and interferons. Today, microbiology is a major participant in global industry, especially in the pharmaceutical, food and chemical industries.

A new era of exploitation of microbial metabolites.

In the past history of the pharmaceutical industry, secondary metabolites have been screened almost exclusively for antimicrobial activities. This biased and narrow view has severely limited the potential application of microbial metabolites. Fortunately, this situation is changing and we are now entering into a new era in which microbial metabolites are being applied to diseases heretofore only subjected to synthetic compounds. This new approach is the application of microbial secondary metabolites to diseases that are not caused by other bacteria or fungi. For years, major drugs such as hypotensive and anti-inflammatory agents that are used for non-infectious diseases have been strictly synthetic products. Similarly, major therapeutics for parasitic diseases in animals (for example, coccidiostats and anthelminthics) resulted strictly from screens of chemically synthesized compounds followed by molecular modification. However, today fermentation products such as monensin and lasalocid dominate the coccidiostat market. The avermectins, another group of streptomycete products, have high activity against helminths and arthropods. Indeed, their activity appears to be an order of magnitude greater than previously discovered anthelminthic agents, the vast majority of which are synthetic compounds. Umezawa's group in Japan has isolated many microbial products with important pharmacological activities by screening with simple enzymic assays. There is much interest in a natural inhibitor of intestinal glucosidase, which is produced by an actinomycete of the genus Actinoplanes. The aim is to decrease hyperglycaemia and triacylglycerol synthesis in adipose tissue, liver and the intestinal wall of patients with diabetes, obesity and type IV hyperlipidaemia. Another natural compound of interest is mevinolin, a fungal product which acts as a cholesterol-lowering agent in animals. Mevinolin is produced by Aspergillus terreus. In its hydroxyacid form (mevinolinic acid), mevinolin is a potent competitive inhibitor of 3-hydroxy-3-methylglutaryl-coenzyme A reductase from liver. It is clear that, although the microbe has contributed greatly to the benefit of mankind, we have merely scratched the surface of the potential of microbial activity.

Achievements in microbial technology.

In 1973, recombinant DNA technology was born and the age of the "new biotechnology" came upon us. Today we are seeing the amazing results of recombinant DNA technology, hybridoma technology, enzyme engineering and protein engineering. These techniques are exerting major effects on basic research and on health care, diagnostics and agriculture and soon will bring about changes in other industries such as petroleum, mining, foods and chemicals. Entire pathways of primary and secondary metabolism have been cloned and expressed in foreign microorganisms. The development of recombinant DNA technology is having its major impact on the production of rare polypeptides such as mammalian enzymes, hormones, antibodies and biological response modifiers. In addition to natural polypeptides, analogs are being produced by recombinant DNA technology and this has added an extra dimension of excitement to the field. The future is thus insured for the expanded use of microorganisms in the biotechnological world and the continued improvement in microbial processes to reduce the cost of drugs, enzymes and specialty chemicals.

Small bugs, big business: the economic power of the microbe.

The versatility of microbial biosynthesis is enormous. The most industrially important primary metabolites are the amino acids, nucleotides, vitamins, solvents, and organic acids. Millions of tons of amino acids are produced each year with a total multibillion dollar market. Many synthetic vitamin production processes are being replaced by microbial fermentations. In addition to the multiple reaction sequences of fermentations, microorganisms are extremely useful in carrying out biotransformation processes. These are becoming essential to the fine chemical industry in the production of single-isomer intermediates. Microbially produced secondary metabolites are extremely important to our health and nutrition. As a group, they have tremendous economic importance. The antibiotic market amounts to almost 30 billion dollars and includes about 160 antibiotics and derivatives such as the beta-lactam peptide antibiotics, the macrolide polyketide erythromycin, tetracyclines, aminoglycosides and others. Other important pharmaceutical products produced by microrganisms are hypocholesterolemic agents, enzyme inhibitors, immunosuppressants and antitumor compounds, some having markets of over 1 billion dollars per year. Agriculturally important secondary metabolites include coccidiostats, animal growth promotants, antihelmintics and biopesticides. The modern biotechnology industry has made a major impact in the business world, biopharmaceuticals (recombinant protein drugs, vaccines and monoclonal antibodies) having a market of 15 billion dollars. Recombinant DNA technology has also produced a revolution in agriculture and has markedly increased markets for microbial enzymes. Molecular manipulations have been added to mutational techniques as means of increasing titers and yields of microbial procresses and in discovery of new drugs. Today, microbiology is a major participant in global industry. The best is yet to come as microbes move into the environmental and energy sectors.

Regulation of ACV synthetase in penicillin- and cephalosporin-producing microorganisms.

ACV synthetase is the first enzyme in the biosynthetic pathway for all natural penicillins and cephalosporins. Its activity catalyzes the possible rate-limiting step and is subject to various regulatory controls. In both the fungus Cephalosporium acremonium and the actinomycete Streptomyces clavuligerus, formation of the enzyme is repressed by ammonium and phosphate ions, but not by easily-utilized carbon sources; it is induced by methionine in C. acremonium. The action of the crude enzyme is indirectly inhibited in vitro by sugars such as glucose and by the carbon source metabolite glyceraldehyde-3-phosphate (G3P). Sugars are not inhibitory to the purified enzyme activity but G3P is inhibitory. The sugar inhibition is reversed by ATP and the G3P inhibition by L-cysteine (L-cys). Addition of L-cys to fermentation media increases beta-lactam production by both microorganisms. Phosphate and ferrous ions inhibit enzyme activity. Dissolved oxygen levels do not affect enzyme formation. Regulation of ACVS formation most likely occurs at the transcriptional level.

Interdependence of gene expression for early steps of cephalosporin synthesis in Streptomyces clavuligerus.

The early steps of cephamycin synthesis by S. clavuligerus are catalyzed sequentially by lysine epsilon-aminotransferase (LAT), delta-(L-alpha-aminoadipyl)-L-cysteinyl-D-valine synthetase (ACVS) and isopenicillin N synthase (cyclase, IPNS). The genes (lat, pcbAB, and pcbC, respectively) are closely linked in the same order as the enzymes act in the biosynthetic pathway and are transcribed in the same direction. Four cephamycin non- (or low-) producing mutants are pleiotropic in that they have undetectable or markedly diminished levels of ACVS and cyclase; two mutants almost completely lack LAT activity. All four mutants are complemented in cephamycin formation by transformation with pNBR1, a plasmid containing a 7.2-kb genomic region of S. clavuligerus in vector pIJ702. The cloned DNA was found to possess no part of the cyclase gene, but instead it contained lat and the 5' upstream part of pcbAB. Doran et al. reported that the 31-bp region between pcbAB and pcbC contains no recognizable promoter or transcription termination sequences. We found that there are 153 bp between the lat ORF and the pcbAB start codon. A potential transcriptional terminator begins 4 to 6 bp downstream of the lat ORF. In the 111-bp segment between the end of the "terminator" and the pcbAB start codon, there are no Streptomyces-like or Escherichia coli-like promoter consensus sequences. However, upstream of the "terminator," that is, in the downstream portion of the lat ORF, are two regions resembling a Streptomyces consensus promoter. Promoter activity in gene fusion constructions was demonstrated in this region. A third potential promoter is upstream of the lat ORF, but only the--10 part is on the cloned DNA. The mechanism by which the cloned DNA (containing lat, the 5' part of pcbAB, and the intervening sequence) influences the expression of the downstream genes encoding ACVS and IPNS, even in strains that possess LAT activity, is an intriguing target of future investigation.

Induction of L-lysine epsilon-aminotransferase by L-lysine in Streptomyces clavuligerus, producer of cephalosporins.

L-Lysine epsilon-aminotransferase (LAT) catalyzes the first reaction in the two-step conversion of L-lysine (Lys) to 1-alpha-aminoadipic acid (Aaa), a direct precursor of cephalosporins (including cephamycin C) in Streptomyces clavuligerus. Previous work showed that addition of Lys to chemically defined medium improved antibiotic production. We show that in S. clavuligerus cultures supplemented with high concentrations of Lys, Lys enhances antibiotic production by a dual effect, i.e. as a substrate of LAT thus providing Aaa and also as an inducer of LAT yielding even more Aaa. On the other hand, LAT is not induced by Aaa.

Phosphate regulation of ACV synthetase and cephalosporin biosynthesis in Streptomyces clavuligerus.

Cephalosporin production by Streptomyces clavuligerus was reduced sharply by 60 mM phosphate added to a chemically-defined medium. All the four synthetases in the pathway examined, i.e., ACV synthetase, cyclase, epimerase and expandase, were repressed by phosphate, with ACV synthetase being the main repression target and expandase the next. ACV synthetase activity was inhibited by phosphate to a lesser extent than expandase and cyclase, and this inhibition could be reversed by adding Fe2+. Fe2+ itself was inhibitory to ACV synthetase action.

Edward P. Abraham, cell-free systems and the fungal biosynthesis of beta-lactams.

Today much is known about the biology of penicillin and cephalosporin production by fungi including the pathways, the biosynthetic enzymes including some crystal structures, the genes and their cloning, expression, sequencing and chromosomal locations, the regulation of the genes and enzymes and even some intelligent guesses about their evolutionary relationships. The key breakthrough that led to rapid progress in these areas was the subcellular work done by EDWARD P. ABRAHAM and his Oxford colleagues in the early 1970s. With his advice and encouragement, my laboratory was able to prepare reliably active soluble cell-free preparations which were instrumental in elucidation of the biosynthetic pathways in fungi (and also in bacteria) by laboratories throughout the world.

Directed biosynthesis of new indolmycins.

Tryptophan in a concentration of 0.4 microgram/ml increased the production of indolmycin by 37%. The lipophilic character of indolmycin was reduced via directed biosynthesis by substituting the aromatic ring system with a methoxy or hydroxy group in the 5-position of the antibiotic. This substitution was achieved by the addition of the corresponding tryptophan and indole precursors to a growing culture of Streptomyces griseus ATCC 12648. The more hydrophilic indolmycin derivatives displayed a moderate increase in antimicrobial activity as compared to indolmycin, but did not markedly change the Gram-positive/Gram-negative ratio of activity. Thin-layer chromatography and mass spectrometry showed that additives substituted in the 6-position were not incorporated into the molecule. Antibiotic titer was reduced by addition of the modified precursors, especially in the case of the precursors substituted in the 6-position.

Effect of solvents on bioconversion of penicillin G to deacetoxycephalosporin G.

The bioconversion of penicillin G, an inexpensive substrate, to the valuable intermediate for semisynthetic cephalosporin production, deacetoxycephalosporin G (DAOG), had been recently shown to be increased by eliminating agitation and adding decane. The present work examining other solvents shows that all alkanes tested are equivalent to decane in activity but that other solvents are either inhibitory or less active than alkanes. Optimum conditions of pH and temperature for the alkane system are not very different from the previously used aqueous system.

Mutational biosynthesis of a new antibiotic, streptomutin A, by an idiotroph of Streptomyces griseus.

Microorganisms producing antibiotics have been genetically converted by earlier workers to mutants which cannot produce antibiotic without supplementation with a moiety of the antibiotic. These antibiotics include neomycin, kanamycin, paromomycin, butirosin, sisomicin, ribostamycin and novobiocin. Success has not been reported for organisms producing guanidinocyclitol antibiotics such as streptomycin. We mutagenized conidia of the streptomycin-producing Streptomyces griseus strain 7-455F3 with nitrosoguanidine at pH 7.0. Non-producers of streptomycin were visually selected by the agar-plug technique using Bacillus subtilis. We successfully isolated mutant MIT-A5 which produces no streptomycin unless streptidine is added to the agar medium. The streptidine-dependent phenotype was confirmed in submerged culture in flasks. Attempts to produce new antibiotics by feeding aminocyclitols to mutant MIT-A5 failed. However a new antibiotic (streptomutin A) was produced by supplementation with the guanidinocyclitol, 2-deoxystreptidine. We propose the term "mutational biosynthesis" for the production of new metabolites by the use of mutants blocked in the biosynthetic pathway to the secondary metabolite. We further propose the term "idiotroph" to properly describe such mutants.