Streptomyces griseolus # 182--a novel organism producing oligomycin antibiotics. Taxonomy, fermentation, and isolation]

Target screening of natural immunosuppressors resulted in isolation of a strain of Streptomyces griseolus (No. 182) producing a complex of antifungal antibiotics. The strain proved to be an aerobe with the growth temperature of 26 to 28 degrees C. Morphological features and physiological properties of the strain were studied. Scanning electron microscopy revealed smooth, oval spores 1.10-1.25 mu in size. The findings showed that the strain belonged to Streptomyces griseolus. Unlike the previously described organisms producing the oligomycin complex the new strain formed straight or twisted sporophores and did not produce melanoid pigment or soluble pigment when grown on the Gauze mineral agar medium No. 1. The procedures for biosynthesis and chemical recovery of the antibiotic complex from the mycelium are described. The complex was shown to include 3 components at a ratio of 80:15:5 identified as oligomycins A, B and C respectively. The oligomycin complex was highly active against Aspergillus niger 137, Tolypocladium inflatum, Fusarium ocsisporum, Curvularia lunata 645 and Trichoderma alba F-32 (MIC 0.1-1.0 mcg/ml). The activity against yeast and bacterial cultures was observed only when the doses were higher than 100 mcg/ml.     

New species of actinomycete Streptomyces variegatus sp. nov. synthesizing an antibiotic of the alpha-hydroxyketopentaene group

Stroptomyces strains INA T-511 and INA 3946 were isolated from 2 different soil samples. Both the strains produced an antibiotic of the group of alpha-hydroxyketopentaenes. The antibiotic was active against gram-positive bacteria, yeasts and fungi belonging to Penicillium. In addition, the strains produced a pigment antibiotic of the prodigiosin type and a pigment identified as ferroverdin. The study of the cultural and morphological features and the natural variation of the strains has shown that they belong to a new species, designated as Streptomyces variegatus sp. nov. Sveshnikova et Timuk.     

Actinoplanes brasiliensis INA 3802--a producer of peptide antibiotics]

In the screening programme for new antibiotics an actinomycete culture designated as 3802 was isolated from a soil sample. The culture produced a complex of peptide antibiotics belonging to the group of lantibiotics. The antibiotic complex included gardimycin (actagardin) and new antibiotics of the same group. By the taxonomic properties strain 3802 was classified as Actinoplanes brasiliensis not previously known to produce gardimycin. Conditions of the antibiotic complex biosynthesis by strain 3802, the isolation methods and biological properties were studied.     

Noncovalent interaction energies in covalent complexes: TEM-1 beta-lactamase and beta-lactams

The class A beta-lactamase TEM-1 is a key bacterial resistance enzyme against beta-lactam antibiotics, but little is known about the energetic bases for complementarity between TEM-1 and its inhibitors. Most inhibitors form a covalent adduct with the catalytic Ser70, making the measurement of equilibrium constants, and hence interaction energies, technically difficult. This study evaluates noncovalent interactions within covalent complexes by examining the differential stability of TEM-1 and its inhibitor adducts. The thermal denaturation of TEM-1 follows a two-state, reversible model with a melting temperature (T(m)) of 51.6C and a van't Hoff enthalpy of unfolding (DeltaH(VH)) of 146.2 kcal/mol at pH 7.0. The stability of the enzyme changes on forming an inhibitor adduct. As expected, some inhibitors stabilize TEM-1; transition-state analogues increase the T(m) by up to 3.7C (1.7 kcal/mol). Surprisingly, all beta-lactam covalent acyl--enzyme complexes tested destabilize TEM-1 significantly relative to the apo-enzyme. For instance, the clinically used inhibitor clavulanic acid and the beta-lactamase-resistant beta-lactams moxalactam and imipenem destabilize TEM-1 by over 2.6C (1.2 kcal/mol) in their covalent adducts. Based on the structure of the TEM-1/imipenem complex (Maveyraud et al., J Am Chem Soc 1998;120:9748--52), destabilization by moxalactam and imipenem is thought to be caused by a steric clash between the side-chain of Asn132 and the 6(7)-alpha group of these beta-lactams. To test this hypothesis, the mutant enzyme N132A was made. In contrast with wild-type, the covalent complexes between N132A and both imipenem and moxalactam stabilize the enzyme, consistent with the hypothesis. To investigate the structural bases of this dramatic change in stability, the structure of N132A/imipenem was determined by X-ray crystallography. In the complex with N132A, imipenem adopts a very different conformation from that observed in the wild-type complex, and the putative destabilizing interaction with residue 132 is relieved. Studies of several enzymes suggest that beta-lactams, and covalent inhibitors in general, can have either net favorable or net unfavorable noncovalent interaction energies within the covalent complex. In the case of TEM-1, such unfavorable interactions convert substrate analogues into very effective inhibitors.     

PHYLOGENETIC POSITION OF CRUSTOMASTIX STIGMATICA SP. NOV. AND DOLICHOMASTIX TENUILEPIS IN RELATION TO THE MAMIELLALES (PRASINOPHYCEAE,CHLOROPHYTA)1

A new marine microalga from the Mediterranean Sea, Crustomastix stigmatica Zingone, is investigated by means of LM, SEM, TEM, and pigment and molecular analyses (nuclear‐encoded small subunit [SSU] rDNA and plastid‐encoded rbcL). Pigment and molecular information is also provided for the related species Dolichomastix tenuilepis Throndsen et Zingone. Crustomastix stigmatica has a bean‐shaped cell body 3–5 μm long and 1.5–2.8 μm wide, with two flagella four to five times the body length. The single chloroplast is pale yellow‐green, cup‐shaped, and lacks a pyrenoid. A small bright yellow stigma is located in the mid‐dorsal part of the cell under the chloroplast membrane. An additional accumulation of osmiophilic globules is at times seen in a chloroplast lobe. Cells lack flat scales, whereas three different types of hair‐like scales are present on the flagella. The main pigments of C. stigmatica are those typical of Mamiellales, though siphonein/siphonaxanthin replaces prasinoxanthin and uriolide is absent. The pigment pool of D. tenuilepis is more similar to that of Micromonas pusilla (Butcher) Manton et Parke and of other Mamiellales. The nuclear SSU rDNA phylogeny shows that the inclusion of C. stigmatica and D. tenuilepis in the Mamiellales retains monophyly for the order. The two species form a distinct clade, which is sister to a clade including all the other Mamiellales. Results of rbcL analyses failed to provide phylogenetic information at both the order and species level. No unique morphological or pigment characteristics circumscribe the mamiellalean clade as a whole nor its two daughter clades.     

Native electrospray mass spectrometry reveals the nature and stoichiometry of pigments in the FMO photosynthetic antenna protein

The nature and stoichiometry of pigments in the Fenna-Matthews-Olson (FMO) photosynthetic antenna protein complex were determined by native electrospray mass spectrometry. The FMO antenna complex was the first chlorophyll-containing protein that was crystallized. Previous results indicate that the FMO protein forms a trimer with seven bacteriochlorophyll a in each monomer. This model has long been a working basis to understand the molecular mechanism of energy transfer through pigment/pigment and pigment/protein coupling. Recent results have suggested, however, that an eighth bacteriochlorophyll is present in some subunits. In this report, a direct mass spectrometry measurement of the molecular weight of the intact FMO protein complex clearly indicates the existence of an eighth pigment, which is assigned as a bacteriochlorophyll a by mass analysis of the complex and HPLC analysis of the pigment. The eighth pigment is found to be easily lost during purification, which results in its partial occupancy in the mass spectra of the intact complex prepared by different procedures. The results are consistent with the recent X-ray structural models. The existence of the eighth bacteriochlorophyll a in this model antenna protein gives new insights into the functional role of the FMO protein and motivates the need for new theoretical and spectroscopic assignments of spectral features of the FMO protein.     

NisT, the transporter of the lantibiotic nisin, can transport fully modified, dehydrated, and unmodified prenisin and fusions of the leader peptide with non-lantibiotic peptides

Lantibiotics are lanthionine-containing peptide antibiotics. Nisin, encoded by nisA, is a pentacyclic lantibiotic produced by some Lactococcus lactis strains. Its thioether rings are posttranslationally introduced by a membrane-bound enzyme complex. This complex is composed of three enzymes: NisB, which dehydrates serines and threonines; NisC, which couples these dehydrated residues to cysteines, thus forming thioether rings; and the transporter NisT. We followed the activity of various combinations of the nisin enzymes by measuring export of secreted peptides using antibodies against the leader peptide and mass spectroscopy for detection. L. lactis expressing the nisABTC genes efficiently produced fully posttranslationally modified prenisin. Strikingly, L. lactis expressing the nisBT genes could produce dehydrated prenisin without thioether rings and a dehydrated form of a non-lantibiotic peptide. In the absence of the biosynthetic NisBC enzymes, the NisT transporter was capable of excreting unmodified prenisin and fusions of the leader peptide with non-lantibiotic peptides. Our data show that NisT specifies a broad spectrum (poly)peptide transporter that can function either in conjunction with or independently from the biosynthetic genes. NisT secretes both unmodified and partially or fully posttranslationally modified forms of prenisin and non-lantibiotic peptides. These results open the way for efficient production of a wide range of peptides with increased stability or novel bioactivities.     

Two ways to skin a cat: acyldepsipeptides antibiotics can kill bacteria through activation or inhibition of ClpP activity

Infection by Mycobacterium tuberculosis (Mtb) has had a devastating effect on the world population. Acyldepsipeptide antibiotics (ADEPs) are known to kill some bacteria by over activating the bacterial ClpP peptidase. ADEP antibiotics also target Mtb, with the assumption that uncontrolled ADEP‐activated proteolysis by ClpP is the common mode of killing. In this issue of Molecular Microbiology, Famulla, et al. now show that ADEP's effectiveness in mycobacteria is likely due to inhibition of ClpP‐dependent protease activity rather than activation. This finding of how the same antibiotic can kill bacteria by either inhibiting or activating proteases illustrates the utility of targeting these enzymes for sorely needed new antibiotics.     

Biosynthesis of β-lactam nuclei in yeast

We have engineered brewer's yeast as a general platform for de novo synthesis of diverse β-lactam nuclei starting from simple sugars, thereby enabling ready access to a number of structurally different antibiotics of significant pharmaceutical importance. The biosynthesis of β-lactam nuclei has received much attention in recent years, while rational engineering of non-native antibiotics-producing microbes to produce β-lactam nuclei remains challenging. Benefited by the integration of heterologous biosynthetic pathways and rationally designed enzymes that catalyze hydrolysis and ring expansion reactions, we succeeded in constructing synthetic yeast cell factories which produce antibiotic cephalosporin C (CPC, 170.1 ± 4.9 μg/g DCW) and the downstream β-lactam nuclei, including 6-amino penicillanic acid (6-APA, 5.3 ± 0.2 mg/g DCW), 7-amino cephalosporanic acid (7-ACA, 6.2 ± 1.1 μg/g DCW) as well as 7-amino desacetoxy cephalosporanic acid (7-ADCA, 1.7 ± 0.1 mg/g DCW). This work established a Saccharomyces cerevisiae platform capable of synthesizing multiple β-lactam nuclei by combining natural and artificial enzymes, which serves as a metabolic tool to produce valuable β-lactam intermediates and new antibiotics.     

Streptoverticillium griseoviridum n. sp., a producer of the candidin-amphotericin B group, antifungal heptaene nonaromatic antibiotic 0185]

An actinomyceteous strain LIA-0185 producing a heptaenic non-aromatic antibiotic of the candidin type was isolated from a soil sample taken in the Georgian SSR under the programme of screening antifungal antibiotics. The taxonomic study of the strain showed that it belonged to the series of viridoflavum and had the following main taxonomic features: the sporophores in the whorls, straight, remote: the aerial mycelium from yellow to dark-olive-grey; the substrate mycelium olive; the soluble pigment absent; the melanine pigment was produced on the peptone medium; the culture formed H2S; assimilated glucose, mannose, inozide and to a lesser extent fructose; did not assimilate arabinose, xylose, sucrose, lactose, ramnose and raffinose. The strain inhibited the growth of yeast and fungi, grampositive bacteria and actinomycetes and produced a complex of non-aromatic heptaenic antibiotics. The actinomycete differed from the other whorl cultures. It was classified as a new species Sv. griseoviridum sp. nov. The antibiotic complex was a mixture of 2 components, i. e. I and II present approximately in equal amounts. Component II was analogous to candidin. Component I was a new original substance.     

IM-2, a butyrolactone autoregulator,induces production of several nucleoside antibiotics in Streptomyces sp. FRI-5

IM-2 is one of the butyrolactone autoregulators of Streptomyces, which triggers production of a blue pigment in Streptomyces sp. FRI-5 at a concentration of 0.6 ng/ml. In the absence of IM-2, Streptomyces sp. FRI-5 was found to produce d-cycloserine. However, the addition of IM-2 at 5-h cultivation stopped both growth and d-cycloserine production, and instead induced production of several different antibiotics. The IM-2-induced antibiotics were isolated from the culture broth, and assigned as the nucleoside antibiotics, showdomycin and minimycin. Therefore, IM-2 was concluded to be a global regulator of a secondary metabolism, which not only induced the production of nucleoside antibiotics but also suppressed d-cycloserine production.     

ESBL-positive strains of the Bacteroides fragilis group isolated from patients at the regional hospital center in Płock (Poland)

The aim of this study was to confirm a presumptive qualification of clinical B. fragilis group strains isolated in P?ock as ESBL-positive strains and to determine some properties of these strains. Twenty four clinical strains belonging to the B. fragilis group, isolated first of all from surgical patients, were received for testing. Identification of strains was performed in the automatic ATB Expression system (bioMerieux sa, France) using biochemical API 20 A strips. Strains were tested for the production of catalase (ID Color Catalase test, bioMerieux sa) and beta-lactamase (Cefinase, BBL, Becton Dickinson, USA). Susceptibility of strains to four antimicrobial agents: clindamycin, metronidazole, amoxicillin/clavulanic acid and imipenem was determined by Etest (AB Biodisk, Sweden). ESBLs were detected with the use of two disc diffusion methods: the double-disc synergy test (DDST) according to Jarlier et al. and the diagnostic disc (DD) test according to Appleton. Seventeen of examined strains belonged to the species Bacteroides fragilis, three--to B. ovatus/thetaiotaomicron, two--to B. distasonis, one--to B. uniformis and one--to B. stercoris/eggerthii. One strain (B. uniformis) did not produce catalase, whereas all strains produced beta-lactamases. Examined strains were susceptible in vitro to metronidazole, amoxicillin/clavulanic acid and imipenem. One clindamycin-resistant strain was detected (B. fragilis). Occurrence of ESBL-type enzymes was confirmed in 22 strains of following species: B. fragilis (17 strains), B. ovatus/thetaiotaomicron (3), B. distasonis (1) and B. uniformis (1). Clinical strains of the B. fragilis group with a new mechanism of resistance to beta-lactam antibiotics appeared during last years in Poland. They produce extended-spectrum beta-lactamases (ESBLs), so they are resistant to penicillins, cephalosporins and monobactams. Monitoring of infections caused by these threatening strains in hospital patients is very important.     

New antibiotic-producing Streptomyces TT-strain,generated by electrical fusion of protoplasts

Interspecific electrofusion between protoplasts of multhiomycin-producing Streptomyces antibioticus aAL Ala⁻Leu⁻ and neomycin-producing S. fradiae fHL His⁻Leu⁻ was done. When the concentration of both protoplasts increased to 1 × 10⁹ protoplasts/ml, the frequency of fusion attained was 18.6%. The addition of multithiomycin and neomycin to the regeneration medium was very effective for screening for fusants able to produce new antibiotics. The ability to produce new antibiotics was very unstable in the fusants. After several subcultures, fusants selected as new antibiotic producers (10 strains) lost this ability with one exception (TT-strain). The antibiotic produced by the stable TT-strain clone was purified and characterized to some extent. It was active on a range of Gram-positive bacteria and distinguished from multhiomycin and neomycin by bioautographic analysis.     

The catalytic efficiency (kcat/Km) of the class A β-lactamase Toho-1 correlates with the thermal stability of its catalytic intermediate analog

The extended-spectrum β-lactamases are associated with antibiotic resistance. Toho-1 R274N/R276N, a Class A β-lactamase of CTX-M-type, efficiently hydrolyzes first generationcephalosporins (for example, cephalothin), in addition to cefotaxime, a third generation cephalosporin. However, this enzyme only marginally hydrolyzes the third generation cephalosporin ceftazidime, and the monobactam aztreonam. The deacylation defectiveness of the mutant Toho-1 E166A/R274N/R276N, which lacks the deacylation activity, results in the accumulation of the complex of an acylated-enzyme intermediate analog. For drug design, it would be useful if a quantitative prediction of a catalytic property were available without the need of enzymatic measurements. Therefore, we examined whether there is a correlation between the thermal stability of a catalytic intermediate (analog) and its kinetic parameters. First we measured the hydrolytic kinetics of the 14 species of β-lactam antibiotics by Toho-1 R274N/R276N, and also measured the thermal stability of the accumulated acyl-intermediates of Toho-1 E166A/R274N/R276 by differential scanning calorimetry. Here we report the correlation of these parameters. The logarithm of the catalytic efficiency for Toho-1 R274N/R276N, log(k_cat/K_m) exhibited the best linear correlation with T_m, which is the heat-denaturation temperature midpoint of the corresponding acylated complex of Toho-1 E166A/R274N/R276N. The correlation coefficient was 0.947, indicating that a relationship exists between the kinetic parameters and the stability of the intermediates. The results demonstrate a new method for investigating the catalytic properties of enzymes against any substrates, and a new approach to designing enzymes.     

Update on macrolide-lincosamide-streptogramin, ketolide, and oxazolidinone resistance genes.

This Minireview summarizes the changes in the field of bacterial resistance to macrolide, lincosamide, streptogramin, ketolide, and oxazolidinone (MLSKO) antibiotics since the nomenclature review in 1999. A total of 66 genes conferring resistance to this group of antibiotics has now been identified and includes 13 new rRNA methylase genes, four ATP-binding transporter genes coding for efflux proteins, and five new inactivating enzymes. During this same time period, 73 new genera carrying known rRNA methylase genes and 87 new genera carrying known efflux and/or inactivating genes have been recognized. The number of bacteria with mutations in the genes for 23S rRNA, L4 and L22 ribosomal proteins, resulting in reduced susceptibility to some members of the group of MLSKO antibiotics has also increased and now includes nine different Gram-positive and 10 different Gram-negative genera. New conjugative transposons carrying different MLSKO genes along with an increased number of antibiotics and/or heavy metal resistance genes have been identified. These mobile elements may play a role in the continued spread of the MLSKO resistance genes into new species, genera, and ecosystems.     

Production of Decolorizing Activity for Molasses Pigment by Coriolus versicolor Ps4a

The distribution of molasses pigment (melanoidin) decolorizing activity (MDA) was investigated in various Basidiomycetes. MDA was only found in some genera of the white-rot-fungi group of which Coriolus versicolor Ps4a showed high activity, a decolorization yield of approximately 80% under the optimal conditions. Production of MDA by C. versicolor was almost completely coincident with the growth of mycelia. The main MDA was due to intracellular enzymes and induced by the molasses pigment. The induced enzyme consisted of two types, namely a sugar dependent enzyme and a sugar independent enzyme. The decolorization by C. versicolor was due to the decomposition of the molasses pigment.     

Fermentation,Isolation and Characterization of Isonitrile Antibiotics

A number of soil isolates belonging to the genus Trichoderma were found to produce isonitrins A, B, C and D and isonitrinic acids E and F, a new class of antibiotics characterized by the presence of isonitrile groups. Taxonomy of the producing organisms, fermentation, isolation and physicochemical and biological properties of isonitrins and isonitrinic acids are reported. Isonitrin A showed the highest in vitro antimicrobial activities against gram-positive and negative bacteria and fungi.     

A new approach for alteration of protease functions: pro-sequence engineering

Several proteases, including the bacterial serine protease subtilisins, require the assistance of the N-terminal pro-sequence of precursors to produce active, mature enzymes. Upon completion of folding, the pro-sequence is autocatalytically degraded because it is not necessary for the activity or stability of folded, mature cognates of the original enzymes. Therefore, the pro-sequence functions as an intramolecular chaperone that guides correct folding of the protease domain. Interestingly, Shinde et al. proposed a new theory of "protein memory" in which an identical polypeptide can fold into an altered conformation with different secondary structure, stability and specificities through a mutated pro-sequence [Shinde et al. (1997) Nature 389:520–522]. We also showed that the autoprocessing efficiency was improved by modifications in the pro-sequence of mutant subtilisins with altered substrate specificity. Further, the pro-sequence from a subtilisin homologue was found to chaperone the intramolecular folding of denatured subtilisin. These results indicate that engineering of the pro-sequence, i.e., site-directed and/or random mutagenesis, chimeras and gene shuffling between members of the family, would be a useful method for improving the functions of autoprocessing proteases. Conventional protein engineering techniques have thus far employed mutagenesis in the protease domain to modify the enzymatic properties. This new approach, which we term "pro-sequence engineering", is not only an important tool for studying the mechanism of protein folding, but also a promising technology for creating unique proteases with various beneficial properties.     

Use of modular,synthetic scaffolds for improved production of glucaric acid in engineered E. coli

The field of metabolic engineering has the potential to produce a wide variety of chemicals in both an inexpensive and ecologically-friendly manner. Heterologous expression of novel combinations of enzymes promises to provide new or improved synthetic routes towards a substantially increased diversity of small molecules. Recently, we constructed a synthetic pathway to produce d-glucaric acid, a molecule that has been deemed a “top-value added chemical” from biomass, starting from glucose. Limiting flux through the pathway is the second recombinant step, catalyzed by myo-inositol oxygenase (MIOX), whose activity is strongly influenced by the concentration of the myo-inositol substrate. To synthetically increase the effective concentration of myo-inositol, polypeptide scaffolds were built from protein–protein interaction domains to co-localize all three pathway enzymes in a designable complex as previously described (Dueber et al., 2009). Glucaric acid titer was found to be strongly affected by the number of scaffold interaction domains targeting upstream Ino1 enzymes, whereas the effect of increased numbers of MIOX-targeted domains was much less significant. We determined that the scaffolds directly increased the specific MIOX activity and that glucaric acid titers were strongly correlated with MIOX activity. Overall, we observed an approximately 5-fold improvement in product titers over the non-scaffolded control, and a 50% improvement over the previously reported highest titers. These results further validate the utility of these synthetic scaffolds as a tool for metabolic engineering.     

14-Fluorobacteriorhodopsin and other fluorinated and 14-substituted analogues. An extra, unusually red-shifted pigment formed during dark adaptation

Five vinyl-substituted fluororetinal analogues (8-F, 10-F, 12-F, 14-F, and 13,14-F2) were found to give bacteriorhodopsin analogues with properties similar to those of the parent system. Of these, only 14-fluororetinal was found to give an extra red-shifted BR analogue (lambda max less than or equal to 680 nm) in equilibrium with the normal 587-nm pigment. The 680-nm pigment was enriched upon irradiation. It rearranged to the 587-nm pigment at room temperature (delta E [symbol: see text] = 20.8 kcal/mol). Chromophore extraction experiments revealed the all-trans geometry for the 680-nm pigment. 14-Chlororetinal gave a similarly red-shifted pigment while 14-methylretinal did not. A scheme for dark adaptation of the 14-halogenated bacteriorhodopsins has been proposed in which the new red-shifted pigment was assigned the all-trans, 15-syn geometry.