Characterization of the cystargolide biosynthetic gene cluster and functional analysis of the methyltransferase CysG

Cystargolides are natural products originally isolated from Kitasatospora cystarginea NRRL B16505 as inhibitors of the proteasome. They are composed of a dipeptide backbone linked to a β-lactone warhead. Recently, we identified the cystargolide biosynthetic gene cluster, but systematic genetic analyses had not been carried out because of the lack of a heterologous expression system. Here, we report the discovery of a homologous cystargolide biosynthetic pathway in Streptomyces durhamensis NRRL-B3309 by genome mining. The gene cluster was cloned via transformation-associated recombination and heterologously expressed in Streptomyces coelicolor M512. We demonstrate that it contains all genes necessary for the production of cystargolide A and B. Single gene deletion experiments reveal that only five of the eight genes from the initially proposed gene cluster are essential for cystargolide synthesis. Additional insights into the cystargolide pathway could be obtained from in vitro assays with CysG and chemical complementation of the respective gene knockout. This could be further supported by the in vitro investigation of the CysG homolog BelI from the belactosin biosynthetic gene cluster. Thereby, we confirm that CysG and BelI catalyze a cryptic SAM-dependent transfer of a methyl group that is critical for the construction of the cystargolide and belactosin β-lactone warheads.

Genome Mining of the Genus Streptacidiphilus for Biosynthetic and Biodegradation Potential

The genus Streptacidiphilus represents a group of acidophilic actinobacteria within the family Streptomycetaceae, and currently encompasses 15 validly named species, which include five recent additions within the last two years. Considering the potential of the related genera within the family, namely Streptomyces and Kitasatospora, these relatively new members of the family can also be a promising source for novel secondary metabolites. At present, 15 genome data for 11 species from this genus are available, which can provide valuable information on their biology including the potential for metabolite production as well as enzymatic activities in comparison to the neighboring taxa. In this study, the genome sequences of 11 Streptacidiphilus species were subjected to the comparative analysis together with selected Streptomyces and Kitasatospora genomes. This study represents the first comprehensive comparative genomic analysis of the genus Streptacidiphilus. The results indicate that the genomes of Streptacidiphilus contained various secondary metabolite (SM) producing biosynthetic gene clusters (BGCs), some of them exclusively identified in Streptacidiphilus only. Several of these clusters may potentially code for SMs that may have a broad range of bioactivities, such as antibacterial, antifungal, antimalarial and antitumor activities. The biodegradation capabilities of Streptacidiphilus were also explored by investigating the hydrolytic enzymes for complex carbohydrates. Although all genomes were enriched with carbohydrate-active enzymes (CAZymes), their numbers in the genomes of some strains such as Streptacidiphilus carbonis NBRC 100919^T were higher as compared to well-known carbohydrate degrading organisms. These distinctive features of each Streptacidiphilus species make them interesting candidates for future studies with respect to their potential for SM production and enzymatic activities.

Genome rearrangements and megaplasmid loss in the filamentous bacterium Kitasatospora viridifaciens are associated with protoplast formation and regeneration

Filamentous Actinobacteria are multicellular bacteria with linear replicons. Kitasatospora viridifaciens DSM 40239 contains a linear 7.8 Mb chromosome and an autonomously replicating plasmid KVP1 of 1.7 Mb. Here we show that lysozyme-induced protoplast formation of the multinucleated mycelium of K. viridifaciens drives morphological diversity. Characterisation and sequencing of an individual revertant colony that had lost the ability to differentiate revealed that the strain had not only lost most of KVP1 but also carried deletions in the right arm of the chromosome. Strikingly, the deletion sites were preceded by insertion sequence elements, suggesting that the rearrangements may have been caused by replicative transposition and homologous recombination between both replicons. These data indicate that protoplast formation is a stressful process that can lead to profound genetic changes.

Versatile Oxidase and Dehydrogenase Activities of Bacterial Pyranose 2-Oxidase Facilitate Redox Cycling with Manganese Peroxidase In Vitro

Pyranose 2-oxidase (POx) has long been accredited a physiological role in lignin degradation, but evidence to provide insights into the biochemical mechanisms and interactions is insufficient. There are ample data in the literature on the oxidase and dehydrogenase activities of POx, yet the biological relevance of this duality could not be established conclusively. Here we present a comprehensive biochemical and phylogenetic characterization of a novel pyranose 2-oxidase from the actinomycetous bacterium Kitasatospora aureofaciens (KaPOx) as well as a possible biomolecular synergism of this enzyme with peroxidases using phenolic model substrates in vitro A phylogenetic analysis of both fungal and bacterial putative POx-encoding sequences revealed their close evolutionary relationship and supports a late horizontal gene transfer of ancestral POx sequences. We successfully expressed and characterized a novel bacterial POx gene from K. aureofaciens, one of the putative POx genes closely related to well-known fungal POx genes. Its biochemical characteristics comply with most of the classical hallmarks of known fungal pyranose 2-oxidases, i.e., reactivity with a range of different monosaccharides as electron donors as well as activity with oxygen, various quinones, and complexed metal ions as electron acceptors. Thus, KaPOx shows the pronounced duality of oxidase and dehydrogenase similar to that of fungal POx. We further performed efficient redox cycling of aromatic lignin model compounds between KaPOx and manganese peroxidase (MnP). In addition, we found a Mn(III) reduction activity in KaPOx, which, in combination with its ability to provide H2O2, implies this and potentially other POx as complementary enzymatic tools for oxidative lignin degradation by specialized peroxidases.IMPORTANCE Establishment of a mechanistic synergism between pyranose oxidase and (manganese) peroxidases represents a vital step in the course of elucidating microbial lignin degradation. Here, the comprehensive characterization of a bacterial pyranose 2-oxidase from Kitasatospora aureofaciens is of particular interest for several reasons. First, the phylogenetic analysis of putative pyranose oxidase genes reveals a widespread occurrence of highly similar enzymes in bacteria. Still, there is only a single report on a bacterial pyranose oxidase, stressing the need of closing this gap in the scientific literature. In addition, the relatively small K. aureofaciens proteome supposedly supplies a limited set of enzymatic functions to realize lignocellulosic biomass degradation. Both enzyme and organism therefore present a viable model to study the mechanisms of bacterial lignin decomposition, elucidate physiologically relevant interactions with specialized peroxidases, and potentially realize biotechnological applications.

Discovery of a Short-Chain ε-Poly-l-lysine and Its Highly Efficient Production via Synthetase Swap Strategy

ε-Poly-l-lysine (ε-PL) is a natural antimicrobial cationic peptide, which is generally recognized as safe for use as a food preservative. To date, the production capacity of strains that produce low-molecular weight ε-PL remains very low and thus unsuitable for industrial production. Here, we report a new low-molecular weight ε-PL-producing Kitasatospora aureofaciens strain. The ε-PL synthase gene of this strain was cloned into a high ε-PL-producing Streptomyces albulus strain. The resulting recombinant strain efficiently produced ε-PL with a molecular weight of 1.3-2.3 kDa and yielded of 23.6 g/L following fed-batch fermentation in a 5 L bioreactor. In addition, circular dichroism spectra showed that this ε-PL takes on a conformation similar to an antiparallel pleated-sheet. Moreover, it demonstrated better antimicrobial activity against yeast compared to the 3.2-4.5 kDa ε-PL. This study provides a highly efficient strategy for production of the low-molecular weight ε-PL, which helps to expand its potential applications.

Exclusivity offers a sound yet practical species criterion for bacteria despite abundant gene flow

BACKGROUND

The question of whether bacterial species objectively exist has long divided microbiologists. A major source of contention stems from the fact that bacteria regularly engage in horizontal gene transfer (HGT), making it difficult to ascertain relatedness and draw boundaries between taxa. A natural way to define taxa is based on exclusivity of relatedness, which applies when members of a taxon are more closely related to each other than they are to any outsider. It is largely unknown whether exclusive bacterial taxa exist when averaging over the genome or are rare due to rampant hybridization.

RESULTS

Here, we analyze a collection of 701 genomes representing a wide variety of environmental isolates from the family Streptomycetaceae, whose members are competent at HGT. We find that the presence/absence of auxiliary genes in the pan-genome displays a hierarchical (tree-like) structure that correlates significantly with the genealogy of the core-genome. Moreover, we identified the existence of many exclusive taxa, although individual genes often contradict these taxa. These conclusions were supported by repeating the analysis on 1,586 genomes belonging to the genus Bacillus. However, despite confirming the existence of exclusive groups (taxa), we were unable to identify an objective threshold at which to assign the rank of species.

CONCLUSIONS

The existence of bacterial taxa is justified by considering average relatedness across the entire genome, as captured by exclusivity, but is rejected if one requires unanimous agreement of all parts of the genome. We propose using exclusivity to delimit taxa and conventional genome similarity thresholds to assign bacterial taxa to the species rank. This approach recognizes species that are phylogenetically meaningful, while also establishing some degree of comparability across species-ranked taxa in different bacterial clades.

Streptacidiphilus hamsterleyensis sp. nov., isolated from a spruce forest soil

Three acidophilic actinobacteria, isolates LSCA2, FGG8 and HSCA14(T), recovered from spruce litter were examined using a polyphasic approach. Chemotaxonomic and morphological properties of the isolates were found to be consistent with their classification in the genus Streptacidiphilus. The isolates were shown to have identical 16S rRNA gene sequences and were most closely related to Streptacidiphilus neutrinimicus DSM 41755(T) (99.9 % similarity). However, DNA:DNA relatedness between isolate HSCA14(T) and the type strain of S. neutrinimicus was found to be low at 44.0 (±14.1) %. A combination of phenotypic features, including degradative and nutritional characteristics were shown to distinguish the isolates from their nearest phylogenetic neighbours. Data from this study show that the isolates form a novel species in the genus for which the name S. hamsterleyensis sp. nov. is proposed. The type strain is HSCA 14(T) (=DSM 45900(T) = KACC 17456(T) = NCIMB 14865(T)).

[Diversity of neutrotolerant acidophilic Streptomycetes isolated from acidic soils in Yunnan Province]

OBJECTIVE

Acidophilic filamentous acitnomycetes are active in the turnover of organic matter in acid litters and soils, and are a source of antifungal antibiotics and acid-stable enzymes. The aim of this study is to delineate the diversity of neutrotolerant acidophilic streptomycetes in acidic soil environment, and to investigate the resources of species.

METHODS

367 actinomycetes with cultural characteristics of streptomycetes were isolated from 14 acidic soil samples collected in Yunnan Province, China, using the method of DDC (dispersion and differential centrifugation) and a selective medium. The isolates were color grouped on the basis of their properties of aerial mycelium, substrate mycelium and diffusible pigments. 97 representative isolates were picked from the color groups for micromorphological observation and for the test of pH range for growth. Among the neutrotolerant acidophilic streptomycetes, 16 representatives were further selected and were subjected to a molecular systematic study based on almost complete 16S rRNA gene sequences and DNA-DNA relatedness.

RESULTS

The isolates were assigned to 12 color groups, and 80% of them were neutrotolerant acidophilic streptomycetes. The 16 representative strains formed eight distinct subclades within the genus of Streptomyces, and probably represented at least eight new genotypic species of Streptomyces.

CONCLUSION

The neutrotolerant acidophilic streptomycetes isolated in this study were placed in eight distinct evolutionary groups, indicating the good diversity and novelty of these microorganisms in acidic soils in Yunnan Province.

Staurosporine and rebeccamycin aglycones are assembled by the oxidative action of StaP, StaC, and RebC on chromopyrrolic acid

In the biosynthesis of the antitumor indolocarbazoles rebeccamycin and staurosporine by streptomycetes, assembly of the aglycones involves a complex set of oxidative condensations. Overall formation of aglycones K252c and arcyriaflavin A from their biosynthetic precursor chromopyrrolic acid involves four- and eight-electron oxidations, respectively. This process is catalyzed by the remarkable enzyme StaP, with StaC and RebC acting to direct the level of oxidation in the newly formed five-membered ring. An aryl-aryl coupling reaction is integral to this transformation as well as oxidative decarboxylation of the dicarboxypyrrole moiety of chromopyrrolic acid. Herein we describe the heterologous expression of staP, staC, and rebC in Escherichia coli and the activity of the corresponding enzymes in constructing the two distinct six-ring scaffolds. StaP is a cytochrome P450 enzyme, requiring dioxygen, ferredoxin, flavodoxin NADP(+)-reductase, and NAD(P)H for activity. StaP on its own converts chromopyrrolic acid into three aglycone products, K252c, arcyriaflavin A, and 7-hydroxy-K252c; in the presence of StaC, K252c is the predominant product, while the presence of RebC directs formation of arcyriaflavin A. (18)O-Labeling studies indicate that the oxygen(s) of the pyrrolinone and maleimide functionalities of the aglycones formed are all derived from dioxygen. This work allowed for the in vitro reconstitution of the full biosynthetic pathway from l-tryptophan to the staurosporine and rebeccamycin aglycones, K252c and 1,11-dichloroarcyriaflavin A.

Substrate specificity of streptomyces transglutaminases

Transglutaminase (TGase) is a multifunctional enzyme vital for many physiologic processes, such as cell differentiation, tissue regeneration, and plant pathogenicity. The acyl transfer function of the enzyme can activate primary amines and, consequently, attach them onto a peptidyl glutamine, a reaction important for various in vivo and in vitro protein crosslinking and modification processes. To understand better the structure-function relationship of the enzyme and to develop it further as an industrial biocatalyst, we studied TGase secreted by several Streptomyces species and Phytophthora cactorum. We purified the enzyme from S. lydicus, S. platensis, S. nigrescens, S. cinnamoneus, and S. hachijoensis. The pH and temperature profiles of S. lydicus, S. platensis, and S. nigrescens TGases were determined. The specificity of S. lydicus TGase toward its acyl-accepting amine substrates was characterized. Correlation of the electronic and steric features of the substrates with their reactivity supported the mechanism previously proposed for Streptomyces mobaraensis TGase.

Remarkable enhancement in PLD activity from Streptoverticillium cinnamoneum by substituting serine residue into the GG/GS motif

The gene that encodes phospholipase D (PLD) from Streptoverticillium cinnamoneum contains three consensus regions (Region I, II and IV as shown in Fig. 1A) that are conserved among the PLD superfamily. The glycine-glycine (GG) motif in Region I and the glycine-serine (GS) motif in Region IV are also conserved in the PLD superfamily. These (GG and GS) motifs are located 7 residues downstream from each HKD motif. In an investigation of fifteen GG/GS motif mutants, generated as fusion proteins with maltose-binding protein (MBP-PLDs), three highly active mutants were identified. Three of the mutants (G215S, G216S, and G216S-S489G) contained a serine residue in the GG motif, and exhibited approximately a 9-27-fold increased transphosphatidylation activity to DPPC compared with recombinant wild type MBP-PLD. When heat stability was compared between three mutants and the recombinant wild type, only G216S-S489G showed heat labile properties. It appears that the 489th serine residue in the GS motif also contributes to the thermal stability of the enzyme. In addition, the GG/GS motif was very close to the active center residue, including two HKD motifs, as shown by computer modeling. The findings suggest that the GG/GS motif of PLD is a key motif that affects catalytic function and enzymatic stability.

Isolation and characterization of four gram-positive nickel-tolerant microorganisms from contaminated sediments

Microbial communities from riparian sediments contaminated with high levels of Ni and U were examined for metal-tolerant microorganisms. Isolation of four aerobic Ni-tolerant, Gram-positive heterotrophic bacteria indicated selection pressure from Ni. These isolates were identified as Arthrobacter oxydans NR-1, Streptomyces galbus NR-2, Streptomyces aureofaciens NR-3, and Kitasatospora cystarginea NR-4 based on partial 16S rDNA sequences. A functional gene microarray containing gene probes for functions associated with biogeochemical cycling, metal homeostasis, and organic contaminant degradation showed little overlap among the four isolates. Fifteen of the genes were detected in all four isolates with only two of these related to metal resistance, specifically to tellurium. Each of the four isolates also displayed resistance to at least one of six antibiotics tested, with resistance to kanamycin, gentamycin, and ciprofloxacin observed in at least two of the isolates. Further characterization of S. aureofaciens NR-3 and K. cystarginea NR-4 demonstrated that both isolates expressed Ni tolerance constitutively. In addition, both were able to grow in higher concentrations of Ni at pH 6 as compared with pH 7 (42.6 and 8.5 mM Ni at pH 6 and 7, respectively). Tolerance to Cd, Co, and Zn was also examined in these two isolates; a similar pH-dependent metal tolerance was observed when grown with Co and Zn. Neither isolate was tolerant to Cd. These findings suggest that Ni is exerting a selection pressure at this site for metal-resistant actinomycetes.

Characterization of the sporulation control protein SsgA by use of an efficient method to create and screen random mutant libraries in streptomycetes

Filamentous actinomycetes are commercially widely used as producers of natural products. However, the mycelial lifestyle of actinomycetes has been a major bottleneck in their commercialization, and screening is difficult due to their poor growth on microtiter plates. We previously demonstrated that the enhanced expression of the cell division activator protein SsgA results in the fragmented growth of streptomycetes, with enhanced growth rates and improved product formation. We here describe a novel and efficient method to create, maintain, and screen mutant libraries in streptomycetes and the application of this method for the functional analysis of Streptomyces coelicolor ssgA. The variants were amplified directly from deep-frozen biomass suspensions. Around 800 ssgA variants, including single-amino-acid-substitution mutants corresponding to more than half of all SsgA residues, were analyzed for their abilities to restore sporulation to an ssgA mutant. The essential residues were clustered in three main sections, and hardly any were in the carboxy-terminal third of the protein. The majority of the crucial residues were conserved among all SsgA-like proteins (SALPs). However, the essential residues L29, D58, and S89 were conserved only in SsgA orthologues and not in other SALPs, suggesting an SsgA-specific function.

Lack of correspondence between genetic and phenotypic groups amongst soil-borne streptomycetes

Correspondence between two distinct genetic traits, 16S rRNA gene sequences and repetitive element-sequence-based BOX-PCR DNA fingerprints, and antibiotic inhibition and resistance phenotypes was explored for a spatially explicit sample of Streptomyces from a prairie soil. There was no correspondence between 16S rRNA gene sequence groups and antibiotic phenotypes. However, 16S rRNA gene sequence groups differed significantly in mean inhibition zone sizes. Specific antibiotic phenotypes may reflect local selection pressures, as suggested by the significant differences in mean inhibition zone sizes against specific test isolates by Streptomyces from the same 16S rRNA gene sequence group but from different locations in soil. Significant correlations between antibiotic phenotypes and BOX-PCR fingerprints were found, but were small (r=0.19-0.22). Although genetic characterizations alone were not predictive of specific antibiotic phenotypes, 16S rRNA gene sequence analyses may identify isolates that are most or least likely to possess substantial inhibitory potential, providing insight into the broad ecological strategy for individual isolates.

Cloning and characterization of a maltotriose-producing α-amylase gene from Thermobifida fusca

The gene (tfa), encoding a maltotriose-producing alpha-amylase from Thermobifida fusca NTU22, was cloned, sequenced and expressed in Escherichia coli. The gene consists of 1,815 base pairs and encodes a protein of 605 amino acids. The base composition of the tfa coding sequence is 69% G+C and the protein has a predicted pI value of 5.5. The deduced amino acid sequence of the tfa amylase exhibited a high degree of similarity with amylases from Thermomonospora curvata and Streptomyces amylases. The purified amylase could be detected as a single band of about 65 kDa by SDS-polyacrylamide gel electrophoresis and this agrees with the predicted size based on the nucleotide sequence. The optimal pH and temperature of the purified amylase were 7.0 and 60 degrees C, respectively. The properties of purified amylase from the E. coli transformant are similar to that of an amylase purified from the original T. fusca NTU22.

Conserved cis-Acting Elements Upstream of Genes Composing the Chitinolytic System of Streptomycetes Are DasR-Responsive Elements

For soil-dwelling bacteria that usually live in a carbon-rich and nitrogen-poor environment, the ability to utilize chitin - the second most abundant polysaccharide on earth - is a decisive evolving advantage as it is a source for both elements. Streptomycetes are high-GC Gram-positive soil bacteria that are equipped with a broad arsenal of chitinase-degrading genes. These genes are induced when the streptomycetes sense the presence of chitooligosaccharides. Their expression is repressed as soon as more readily assimilated carbon sources become available. This includes for example glucose or N-acetylglucosamine, the monomer subunit of chitin. Historically, the first cis-acting elements involved in carbon regulation in streptomycetes were found more than a decade ago upstream of chitinase genes, but the transcriptional regulator had so far remained undiscovered. In this work, we show that these cis-acting elements consist of inverted repeats with multiple occurrences and are bound by the HutC/GntR type regulator DasR. We have therefore designated these sites as DasR-responsive elements (dre). DasR, which is also the repressor of the genes for the N-acetylglucosamine-specific phosphotransferase transport system, should therefore play a critical role in sensing the balance between the monomeric and polymeric forms of N-acetylglucosamine.

Phylogenetic diversity of acidophilic sporoactinobacteria isolated from various soils

Spore forming actinobacteria (sporoactinobacteria) isolated from soils with an acidic pH in Pinus thunbergii forests and coal mine waste were subjected to taxonomic characterization. For the isolation of acidophilic actinobacteria, acidified starch casein agar (pH adjusted to 4-5) was used. The numbers of actinobacteria growing in acidic media were between 3.2 x 10(4) and 8.0 x 10(6) CFU/g soil. Forty three acidophilic actinobacterial strains were isolated and their 16S rDNA sequences were determined. The isolates were divided into eight distinctive phylogenetic clusters within the variation encompassed by the family Streptomycetaceae. Four clusters among them were assigned to the genus Streptacidiphilus, whereas the remaining four were assigned to Streptomyces. The clusters belonging to either Streptomyces or Streptacidiphilus did not form monophyletic clade. The growth pH profiles indicated that the representative isolates grew best between pH 5 and 6. It is evident from this study that acidity has played a critical role in the differentiation of the family Streptomycetaceae, and also that different mechanisms might have resulted in the evolution of two groups, Streptacidiphilus (strict acidophiles) and neutrotolerant acidophilic Streptomyces. The effect of geographic separation was clearly seen among the Streptacidiphilus isolates, which may be a key factor in speciation of the genus.

'Candidatus Streptomyces philanthi', an endosymbiotic streptomycete in the antennae of Philanthus digger wasps

Symbiotic interactions with bacteria are essential for the survival and reproduction of many insects. The European beewolf (Philanthus triangulum, Hymenoptera, Crabronidae) engages in a highly specific association with bacteria of the genus Streptomyces that appears to protect beewolf offspring against infection by pathogens. Using transmission and scanning electron microscopy, the bacteria were located in the antennal glands of female wasps, where they form dense cell clusters. Using genetic methods, closely related streptomycetes were found in the antennae of 27 Philanthus species (including two subspecies of P. triangulum from distant localities). In contrast, no endosymbionts could be detected in the antennae of other genera within the subfamily Philanthinae (Aphilanthops, Clypeadon and Cerceris). On the basis of morphological, genetic and ecological data, 'Candidatus Streptomyces philanthi' is proposed. 16S rRNA gene sequence data are provided for 28 ecotypes of 'Candidatus Streptomyces philanthi' that reside in different host species and subspecies of the genus Philanthus. Primers for the selective amplification of 'Candidatus Streptomyces philanthi' and an oligonucleotide probe for specific detection by fluorescence in situ hybridization (FISH) are described.

Fatal pulmonary infection associated with a novel organism, "para-streptomyces abscessus"

Actinomycetes are increasingly recognized as pathogenic in the immunocompromised host. We isolated an asporogenous, nonmotile, aerobic gram-positive rod from a transplant recipient with a fatal pulmonary infection. The pathology was similar to that associated with Rhodococcus equi, including intra-histiocytic localization. The organism was relatively inert in standard biochemical tests. 16S rRNA gene sequencing indicated a potentially unique organism most closely related to the genus Streptomyces, for which we propose the name "Para-streptomyces abscessus."

[High expression of mirobial transglutaminase gene from Streptoverticillium mobaraense in Escherichia coli]

The microbial transglutamunase (MTG) gene was amplified from the genomic DNA of Streptoverticillium mobaraensea by using PCR and inserted into pET vector to construct the expression plasmid called pET-MTG. The pET-MTG was transfected into E. coli (Rosetta DE3) and the MTG protein was found to be highly expressed as inclusion bodies. The inclusion bodies were isolated and subjected to denaturation and re-naturation, followed by strong cation ion-exchange chromatography to purify the expressed MTG. The specific activity of purified MTG was close to that of native MTG. Taken together, this study might provide a base for the industrial production of microbial transglutaminase.

Regulation of secondary metabolism in streptomycetes

While the biological functions of most of the secondary metabolites made by streptomycetes are not known, it is inconceivable that they do not play an adaptive ecological role. The biosynthesis of secondary metabolites under laboratory conditions usually occurs in a growth phase or developmentally controlled manner, but is also influenced by a wide variety of environmental and physiological signals, presumably reflecting the range of conditions that trigger their production in nature. The expression of secondary metabolic gene clusters is controlled by many different families of regulatory proteins, some of which are found only in actinomycetes, and is elicited by both extracellular and intracellular signalling molecules. The application of a variety of genetic and molecular approaches is now beginning to reveal fascinating insights into the complex regulatory cascades that govern this process.

Culturable marine actinomycete diversity from tropical Pacific Ocean sediments

Actinomycetes were cultivated using a variety of media and selective isolation techniques from 275 marine samples collected around the island of Guam. In total, 6425 actinomycete colonies were observed and 983 (15%) of these, representing the range of morphological diversity observed from each sample, were obtained in pure culture. The majority of the strains isolated (58%) required seawater for growth indicating a high degree of marine adaptation. The dominant actinomycete recovered (568 strains) belonged to the seawater-requiring marine taxon 'Salinospora', a new genus within the family Micromonosporaceae. A formal description of this taxon has been accepted for publication (Maldonado et al., 2005) and includes a revision of the generic epithet to Salinispora gen. nov. Members of two major new clades related to Streptomyces spp., tentatively called MAR2 and MAR3, were cultivated and appear to represent new genera within the Streptomycetaceae. In total, five new marine phylotypes, including two within the Thermomonosporaceae that appear to represent new taxa, were obtained in culture. These results support the existence of taxonomically diverse populations of phylogenetically distinct actinomycetes residing in the marine environment. These bacteria can be readily cultured using low nutrient media and represent an unexplored resource for pharmaceutical drug discovery.

Grouping of streptomycetes using 16S-ITS RFLP fingerprinting

A total of 463 Streptomyces and Kitasatospora type strains were screened using 16S-ITS RFLP fingerprinting (combined restriction digest using enzymes BstUI and HaeIII). In total, 59 clusters could be delineated, each comprising multiple strains with nearly identical patterns. Good correlation was found in general with phylogeny, as revealed by 16S rDNA sequencing. Most strains assigned to a particular 16S-ITS RFLP cluster were classified into the corresponding 16S sequencing cluster whether a 16S similarity cut-off value of 97 or 98% was used. We conclude that the taxonomic resolution of 16S-ITS RFLP fingerprinting is higher than that of 16S rDNA sequencing; this may provide a tool for reducing the number of laborious DNA-DNA hybridizations necessary for discovering potentially new species within Streptomyces.

The bacterial paromomycin resistance gene, aphH, as a dominant selectable marker in Volvox carteri

The aminoglycoside antibiotic paromomycin that is highly toxic to the green alga Volvox carteri is efficiently inactivated by aminoglycoside 3'-phosphotransferase from Streptomyces rimosus. Therefore, we made constructs in which the bacterial aphH gene encoding this enzyme was combined with Volvox cis-regulatory elements in an attempt to develop a new dominant selectable marker--paromomycin resistance (PmR)--for use in Volvox nuclear transformation. The construct that provided the most efficient transformation was one in which aphH was placed between a chimeric promoter that was generated by fusing the Volvox hsp70 and rbcS3 promoters and the 3' UTR of the Volvox rbcS3 gene. When this plasmid was used in combination with a high-impact biolistic device, the frequency of stable PmR transformants ranged about 15 per 106 target cells. Due to rapid and sharp selection, PmR transformants were readily isolated after six days, which is half the time required for previously used markers. Co-transformation of an unselected marker ranged about 30%. The chimeric aphH gene was stably integrated into the Volvox genome, frequently as tandem multiple copies, and was expressed at a level that made selection of PmR transformants simple and unambiguous. This makes the engineered bacterial aphH gene an efficient dominant selection marker for the transformation and co-transformation of a broad range of V. carteri strains without the recurring need for using auxotrophic recipient strains.

Two minimal Tat translocases in Bacillus

Activity of the Tat machinery for protein transport across the inner membrane of Escherichia coli and the chloroplast thylakoidal membrane requires the presence of three membrane proteins: TatA, TatB and TatC. Here, we show that the Tat machinery of the Gram-positive bacterium Bacillus subtilis is very different because it contains at least two minimal Tat translocases, each composed of one specific TatA and one specific TatC component. A third, TatB-like component is apparently not required. This implies that TatA proteins of B. subtilis perform the functions of both TatA and TatB of E. coli and thylakoids. Notably, the two B. subtilis translocases named TatAdCd and TatAyCy both function as individual, substrate-specific translocases for the twin-arginine preproteins PhoD and YwbN, respectively. Importantly, these minimal TatAC translocases of B. subtilis are representative for the Tat machinery of the vast majority of Gram-positive bacteria, Streptomycetes being the only known exception with TatABC translocases.

Kitasatospora viridis sp. nov., a novel actinomycete from soil

The taxonomic position of a rhizosphere isolate, strain 52108a(T), was determined using a polyphasic approach. The strain was found to have chemical and morphological properties consistent with its assignment to the genus Kitasatospora. An almost complete 16S rRNA gene sequence determined for the strain was aligned with corresponding sequences of representatives of the genus Kitasatospora and related taxa using three tree-making algorithms. The organism formed a distinct phyletic line within the Kitasatospora clade and was most closely related to Kitasatospora arboriphila (98.9 %), Kitasatospora kifunensis (99.0 %), Kitasatospora paracochleata (98.4 %) and Kitasatospora terrestris (98.2 %), but was readily distinguished from representatives of these species using a combination of phenotypic properties. The combined genotypic and phenotypic data show that the strain should be classified in the genus Kitasatospora as a novel species. The name proposed is Kitasatospora viridis sp. nov., with the type strain 52108a(T) (=AS 4.1878(T)=DSM 44826(T)).

High level expression of Streptomyces mobaraensis transglutaminase in Corynebacterium glutamicum using a chimeric pro-region from Streptomyces cinnamoneus transglutaminase

We previously observed secretion of native-type Streptomyces mobaraensis transglutaminase (MTGase) in Corynebacterium glutamicum by co-expressing the subtilisin-like protease SAM-P45 from S. albogriseolus which processes the pro-region. In the present study, we have used a chimeric pro-region consisting of S. mobaraensis and Streptomyces cinnamoneus transglutaminases for the production of MTGase in C. glutamicum. As a result, secretion of MTGase using the chimeric pro-region is increased compared to that using the native pro-region.

[Construction of efficient conjugal plasmids between Escherichia coli and Streptomycetes]

Conjugal plasmid pGH112 has been developed based on the replicons of Streptomyces coelicolor plasmid SCP2 and E. coli ColE. The plasmid contains ampicilin resistance gene(amp) for selection in E. coli and thiostrepton resistance gene (tsr) for selection in Streptomycetes, and a 0.76 kb oriT fragment of (IncP) RK2. Conjugal transfer of pGH112 was performed from E. coli to S. coelicolor A3(2), S. avermitilis, S. lividans TK54, S. toxytricini NNRL15443, S. venezuelae ISP5230 and Sacc. erythraea by conjugation, results show that the plasmid was able to transfer efficenctly from E. coli to Streptomycetes, was stably inherited in the recipients. pGH113 was constructed from pGH112 by combining the constitutive ermE promoter with green fluorescent protein gene(gfp).

Streptacidiphilus jiangxiensis sp. nov., a novel actinomycete isolated from acidic rhizosphere soil in China

The taxonomic position of three acidophilic actinomycetes isolated from acidic rhizosphere soil was established using a polyphasic approach. The morphological and chemical properties of the isolates were found to be consistent with their assignment to the genus Streptacidiphilus. Almost complete 16S rRNA gene sequences determined for the strains were aligned with corresponding sequences of representatives of the genera Kitasatospora, Streptacidiphilus and Streptomyces and phylogenetic trees inferred using three tree-making algorithms. The organisms formed a distinct subclade within the Streptacidiphilus 16S rRNA gene tree. They also shared nearly identical phenotypic profiles and rep-PCR fingerprint patterns that readily distinguished them from representatives of the established species of Streptacidiphilus. It is evident from the genotypic and phenotypic data that the three isolates form a new species in the genus Streptacidiphilus. The name proposed for this new species is Streptacidiphilus jiangxiensis, the type strain is isolate 33214T (= AS 4.1857T = JCM 12277T).

Phylogenetic analysis of the genera Streptomyces and Kitasatospora based on partial RNA polymerase beta-subunit gene (rpoB) sequences

The RNA polymerase beta-subunit genes (rpoB) of 67 Streptomyces strains, representing 57 species, five Kitasatospora strains and Micromonospora echinospora KCTC 9549 were partially sequenced using a pair of rpoB PCR primers. Among the streptomycetes, 99.7-100 % similarity within the same species and 90.2-99.3 % similarity at the interspecific level were observed by analysis of the determined rpoB sequences. The topology of the phylogenetic tree based on rpoB sequences was similar to that of 16S rDNA. The five Kitasatospora strains formed a stable monophyletic clade and a sister group to the clade comprising all Streptomyces species. Although there were several discrepancies in the details, considerable agreement was found between the results of rpoB analysis and those of numerical phenetic classification. This study demonstrates that analysis of rpoB can be used as an alternative genetic method in parallel to conventional taxonomic methods, including numerical phenetic and 16S rDNA analyses, for the phylogenetic analyses of the genera Streptomyces and Kitasatospora.

Genetic and phenotypic traits of streptomycetes used to characterize antibiotic activities of field-collected microbes

Although antibiotic production may contribute significantly to microbial fitness, there is limited information on the ecology of antibiotic-producing microbial populations in soil. Indeed, quantitative information on the variation in frequency and intensity of specific antibiotic inhibitory and resistance abilities within soil microbial communities is lacking. Among the streptomycetes, antibiotic production is highly variable and resistance to antibiotics is highly specific to individual microbial strains. The objective of this work was to genetically and phenotypically characterize a reference collection of streptomycetes for use in distinguishing inhibition and resistance phenotypes of field-collected microbes. Specifically, we examined inhibition and resistance abilities of all isolates in all possible pairwise combinations, genetic relatedness using BOX-PCR and 16S rDNA sequence analyses, nutrient utilization profiles, and antibiotic induction among all possible three-way combinations of isolates. Each streptomycete isolate possessed a unique set of phenotypic and genetic characteristics. However, there was little correspondence between phenotypic and genetic traits. This collection of reference isolates provides the potential for distinguishing 1024 inhibition and resistance phenotypes in field-collected microbes. Relationships between the genetic and phenotypic characteristics examined may provide preliminary insight into the distinct strategies that microbes use in optimizing their fitness in natural environments.Key words: antibiotic inhibition, resistance, nutrient utilization, BOX-PCR, 16S rDNA.

Isolation and identification of actinobacteria from surface-sterilized wheat roots

This is the first report of filamentous actinobacteria isolated from surface-sterilized root tissues of healthy wheat plants (Triticum aestivum L.). Wheat roots from a range of sites across South Australia were used as the source material for the isolation of the endophytic actinobacteria. Roots were surface-sterilized by using ethanol and sodium hypochlorite prior to the isolation of the actinobacteria. Forty-nine of these isolates were identified by using 16S ribosomal DNA (rDNA) sequencing and found to belong to a small group of actinobacterial genera including Streptomyces, Microbispora, Micromonospora, and Nocardiodes spp. Many of the Streptomyces spp. were found to be similar, on the basis of their 16S rDNA gene sequence, to Streptomyces spp. that had been isolated from potato scabs. In particular, several isolates exhibited high 16S rDNA gene sequence homology to Streptomyces caviscabies and S. setonii. None of these isolates, nor the S. caviscabies and S. setonii type strains, were found to carry the nec1 pathogenicity-associated gene or to produce the toxin thaxtomin, indicating that they were nonpathogenic. These isolates were recovered from healthy plants over a range of geographically and temporally isolated sampling events and constitute an important plant-microbe interaction.

Taxonomic re-evaluation of whorl-forming Streptomyces (formerly Streptoverticillium) species by using phenotypes, DNA-DNA hybridization and sequences of gyrB, and proposal of Streptomyces luteireticuli (ex Katoh and Arai 1957) corrig., sp. nov., nom. rev

The taxonomic status of 64 strains of whorl-forming Streptomyces (formerly Streptoverticillium) species was re-evaluated and strains were reclassified on the basis of their phenotypes, DNA-DNA hybridization data and partial sequences of gyrB, the structural gene of the B subunit of DNA gyrase. These strains, which consisted of 46 species and eight subspecies with validly published names and 13 species whose names have not been validly published [including 10 strains examined by the International Streptomyces Project (ISP)], were divided into two groups, namely typical and atypical whorl-forming Streptomyces species, based on their phenotypes and gyrB gene sequences. The typical whorl-forming species (59 strains) were divided into six major clusters of three or more species, seven minor clusters of two species and five single-member clusters, based on the threshold value of 97 % gyrB sequence similarity. Major clusters were typified by Streptomyces abikoensis, Streptomyces cinnamoneus, Streptomyces distallicus, Streptomyces griseocarneus, Streptomyces hiroshimensis and Streptomyces netropsis. Phenotypically, members of each cluster resembled each other closely except for the S. distallicus cluster, which was divided phenotypically into the S. distallicus and Streptomyces stramineus subclusters, and the S. netropsis cluster, which was divided into the S. netropsis and Streptomyces eurocidicus subclusters. Strains in each minor cluster closely resembled each other phenotypically. DNA-DNA relatedness between the representative species and others in each major cluster and/or subcluster, and between strains in the minor clusters, was >70 %, indicating that the major clusters and/or subclusters and the minor clusters each comprise a single species. It was concluded that 59 strains of typical whorl-forming Streptomyces species consisted of the following 18 species, including subjective synonym(s): S. abikoensis, Streptomyces ardus, Streptomyces blastmyceticus, S. cinnamoneus, S. eurocidicus, S. griseocarneus, S. hiroshimensis, Streptomyces lilacinus, 'Streptomyces luteoreticuli', Streptomyces luteosporeus, Streptomyces mashuensis, Streptomyces mobaraensis, Streptomyces morookaense, S. netropsis, Streptomyces orinoci, S. stramineus, Streptomyces thioluteus and Streptomyces viridiflavus.

Streptacidiphilus gen. nov., acidophilic actinomycetes with wall chemotype I and emendation of the family Streptomycetaceae (Waksman and Henrici (1943)AL) emend. Rainey et al. 1997

The taxonomic position of acidophilic actinomycetes selectively isolated from acidic soils and litter was examined using a polyphasic approach. The distinct 16S rDNA phyletic branch formed by representative strains was equated with related monophyletic clades that corresponded to the genera Kitasatospora and Streptomyces. The acidophilic isolates also exhibited a distinctive pH profile, a unique 16S rDNA signature, and contained major amounts of LL-diaminopimelic acid, galactose and rhamnose in whole-organism hydrolysates. It is proposed that these acidophilic actinomycetes be assigned to a new genus, Streptacidiphilus gen. nov., on the basis of genotypic and phenotypic differences. Three species were defined on the basis of DNA:DNA pairing and phenotypic data, namely, Streptacidiphilus albus sp. nov., the type species, Streptacidiphilus neutrinimicus sp. nov. and Streptacidiphilus carbonis sp. nov. Members of the genera Kitasatospora, Streptacidiphilus and Streptomyces share a number of key characteristics and form a stable monophyletic branch in the 16S rDNA tree. It is, therefore, proposed that the description of the family Streptomycetaceae be emended to account for properties shown by Kitasatospora and Streptacidiphilus species.

Structure of folding intermediates at pH 4.0 and native state of microbial transglutaminase

Recombinant microbial transglutaminase has been expressed in Escherichia coli as insoluble inclusion bodies. After we searched for refolding conditions, refolding of the protein could be done by first dilution of the unfolded enzyme in a buffer at pH 4.0, and then by titration of the pH from 4.0 to 6.0. CD analysis showed that a burst of secondary structure formation occurred within the dead time of the experiment and accounted for 75% of the signal change in the far UV CD, with little tertiary structure being formed. This burst was followed by slow rearrangement of the secondary structure accompanied by formation of tertiary structure. The secondary and tertiary structures of the final sample at pH 4.0, corresponding to the folding intermediate, were different from these structures at pH 6.0. Once the native structure was obtained, acidification of the native protein to pH 4.0 did not lead to a structure like that of the folding intermediate. Sedimentation velocity analysis showed that the folding intermediate had an expanded structure and contained no other structure species including large aggregates.

Secretion of active-form Streptoverticillium mobaraense transglutaminase by Corynebacterium glutamicum: processing of the pro-transglutaminase by a cosecreted subtilisin-Like protease from Streptomyces albogriseolus

The transglutaminase secreted by Streptoverticillium mobaraense is a useful enzyme in the food industry. A fragment of transglutaminase was secreted by Corynebacterium glutamicum when it was coupled on a plasmid to the promoter and signal peptide of a cell surface protein from C. glutamicum. We analyzed the signal peptide and the pro-domain of the transglutaminase gene and found that the signal peptide consists of 31 amino acid residues and the pro-domain consists of 45 residues. When the pro-domain of the transglutaminase was used, the pro-transglutaminase was secreted efficiently by C. glutamicum but had no enzymatic activity. However, when the plasmid carrying the S. mobaraense transglutaminase also encoded SAM-P45, a subtilisin-like serine protease derived from Streptomyces albogriseolus, the peptide bond to the C side of 41-Ser of the pro-transglutaminase was hydrolyzed, and the pro-transglutaminase was converted to an active form. Our findings suggest that C. glutamicum has potential as a host for industrial-scale protein production.

Description of two novel species of the genus Kitasatospora Omura et al. 1982, Kitasatospora cineracea sp. nov. and Kitasatospora niigatensis sp. nov

Five actinomycete strains, SK-3255T, SK-3406T, SK-3412, SK-3421 and OM-5023, were isolated using a novobiocin-containing agar medium from soil samples. These strains produced long spore chains on aerial mycelium and contained LL- and meso-diaminopimelic acids (DAPs) in the cell wall. On the basis of morphological and chemotaxonomic characteristics and phylogenetic analysis, these five strains were classified into the genus Kitasatospora. DNA-DNA hybridization and comparison of physiological characteristics revealed that strains SK-3255T and SK-3406T differed from known species. Strains SK-3406T, SK-3412 and SK-3421 were regarded as the same species. Strain OM-5023 was identified as Kitasatospora griseola. Therefore, two novel species are proposed, Kitasatospora cineracea sp. nov. and Kitasatospora niigatensis sp. nov., with the type strains K. cineracea SK-3255T (= IFO 16452T = JCM 10915T = NRRL B-23134T) and K. niigatensis SK-3406T (= IFO 16453T = JCM 10916T = NRRL B-24135T).

Primary metabolism and its control in streptomycetes: a most unusual group of bacteria

Streptomycetes are Gram-positive bacteria with a unique capacity for the production of a multitude of varied and complex secondary metabolites. They also have a complex life cycle including differentiation into at least three distinct cell types. Whilst much attention has been paid to the pathways and regulation of secondary metabolism, less has been paid to the pathways and the regulation of primary metabolism, which supplies the precursors. With the imminent completion of the total genome sequence of Streptomyces coelicolor A3(2), we need to understand the pathways of primary metabolism if we are to understand the role of newly discovered genes. This review is written as a contribution to supplying these wants. Streptomycetes inhabit soil, which, because of the high numbers of microbial competitors, is an oligotrophic environment. Soil nutrient levels reflect the fact that plant-derived material is the main nutrient input; i.e. it is carbon-rich and nitrogen- and phosphate-poor. Control of streptomycete primary metabolism reflects the nutrient availability. The variety and multiplicity of carbohydrate catabolic pathways reflects the variety and multiplicity of carbohydrates in the soil. This multiplicity of pathways has led to investment by streptomycetes in pathway-specific and global regulatory networks such as glucose repression. The mechanism of glucose repression is clearly different from that in other bacteria. Streptomycetes feed by secreting complexes of extracellular enzymes that break down plant cell walls to release nutrients. The induction of these enzyme complexes is often coordinated by inducers that bear no structural relation to the substrate or product of any particular enzyme in the complex; e.g. a product of xylan breakdown may induce cellulase production. Control of amino acid catabolism reflects the relative absence of nitrogen catabolites in soil. The cognate amino acid induces about half of the catabolic pathways and half are constitutive. There are reduced instances of global carbon and nitrogen catabolite control of amino acid catabolism, which again presumably reflects the relative rarity of the catabolites. There are few examples of feedback repression of amino acid biosynthesis. Again this is taken as a reflection of the oligotrophic nature of the streptomycete ecological niche. As amino acids are not present in the environment, streptomycetes have rarely invested in feedback repression. Exceptions to this generalization are the arginine and branched-chain amino acid pathways and some parts of the aromatic amino acid pathways which have regulatory systems similar to Escherichia coli and Bacillus subtilis and other copiotrophic bacteria.

Overproduction of microbial transglutaminase in Escherichia coli, in vitro refolding, and characterization of the refolded form

(MTG) The Streptoverticillium transglutaminase gene, synthesized previously for yeast expression, was modified and resynthesized for overexpression in E. coli. A high-level expression plasmid, pUCTRPMTG-02(+), was constructed. Furthermore, to eliminate the N-terminal methionine, pUCTRPMTGD2 was constructed. Cultivation of E. coli transformed with pUCTRPMTG02(+) or pUCTRPMTGD2 yielded a large amount of MTG (200-300 mg/liter) as insoluble inclusion bodies. The N-terminal amino acid residue of the expressed protein was methionine or serine (the second amino acid residue of the mature MTG sequence), respectively. Transformed E. coli cells were disrupted, and collected pellets of inclusion bodies were solubilized with 8 M urea. Rapid dilution treatment of solubilized MTG restored the enzymatic activity. Refolded MTG, purified by ion-exchange chromatography, which had an N-terminal methionine or serine residue, showed activity equivalent to that of native MTG. These results indicated that recombinant MTG could be produced efficiently in E. coli.

Sequence analysis of domains III and IV of the 23S rRNA gene of verticillate streptomycetes

Domains III and IV of the 23S rRNA gene of 25 strains of verticillate streptomycetes were sequenced. None of the sequences was identical to any other, with regions of variability being restricted to parts of helices 54 and 64. No relationships were detected between the similarities in the sequence and the assignment to phenetic clusters as defined by the numerical taxonomy studies. Limited agreement was also found between similarity of the sequences and DNA-DNA homology values. However, species (> 70% DNA-DNA homology values)-specific diagnostic oligonucleotides generally could be defined, except for Streptomyces baldaccii. Therefore the determination of the 23S rRNA sequence may be of greater value for fingerprinting individual strains than for taxonomic or identification purposes.

Kitasatospora cheerisanensis sp. nov., a new species of the genus Kitasatospora that produces an antifungal agent

An actinomycete, strain YC75T, which produced bafilomycin-like antifungal compounds, was identified as a member of the genus Kitasatospora on the basis of morphological and chemotaxonomic characteristics. The strain produced the aerial and fragmenting vegetative mycelia consisting of straight chains of 20 or more smooth-surfaced spores. Submerged spores were formed in tryptic soy broth. No soluble pigments were formed. Whole-cell hydrolysates contained glucose and mannose, but not galactose. The 16S rDNA sequence of YC75T was compared with those of the other representative kitasatosporae and streptomycetes. Strain YC75T formed a significant monophyletic clade with Kitasatospora phosalacinea. The levels of DNA relatedness between strain YC75T and representatives of the genus Kitasatospora ranged from 16 to 59% including K. phosalacinea (28 and 40%). It is clear from polyphasic evidence that the isolate should be classified as Kitasatospora cheerisanensis sp. nov., whose type strain is YC75T (= KCTC 2395T). The presence of galactose in whole-cell hydrolysates may not be a stable chemical marker for the genus Kitasatospora.

Purification, characterization, and sequence determination of phospholipase D secreted by Streptoverticillium cinnamoneum

Phospholipase D (PLD), secreted into the culture medium of an actinomycete, Streptoverticillium cinnamoneum, has been purified to homogeneity and characterized. The Stv. cinnamoneum PLD efficiently catalyzes both the hydrolysis and transphosphatidylation of various phospholipids, including phosphatidylethanolamine (PE), phosphatidylcholine (PC), and phosphatidylserine (PS). However, the substrate specificity differs between the two reactions; PE serves as the most preferred substrate for the hydrolysis, but PC and PS are better substrates than PE for the transphosphatidylation. In addition, the transphosphatidylation but not the hydrolysis of PE and PC is markedly activated on the addition of metal ions, especially Al3+. Nucleotide and amino acid sequence determination of the Stv. cinnamoneum PLD revealed the presence of common structural motifs identified in all PLD sequences from various species.

Rare, suppurative pulmonary infection caused by Nocardiopsis dassonvillei recognized by glycolipid markers

An opportunistic actinomycete was isolated as the only etiological agent of a severe, suppurative pulmonary infection. The strain was rapidly recognised as Nocardiopsis by the taxonomically important and immunologically active glycolipid markers (G1 and G2). Identification of the clinical isolate, from a group of actinomycetes mainly known as soil habitants, was definitely proved by chemotaxonomic studies (cell wall/sugar, phospholipid and fatty acid types) as well as by genomic data (GC content, DNA-DNA reassociation). The level of DNA-DNA homology of the clinical actinomycete, in comparison with other reference members of this genus, revealed the highest (88%) relatedness to Nocardiopsis dassonvillei. The results confirmed the value and generic specificity of glycolipid markers from Nocardiopsis, the first time used for rapid recognition of a clinical strain causing a nocardiosis-like disease.

Purification, characterisation, and gene cloning of transglutaminase from Streptoverticillium cinnamoneum CBS 683.68

The transglutaminase (TGase; EC 2.3.2.13) from Streptoverticillium cinnamoneum CBS 683.68 has been purified, characterised and its gene cloned. The purified enzyme had a relative molecular mass of 37,660 determined by mass spectrometry and contained a single Cys residue that was essential for the catalytic activity. Contrary to eukaryotic TGases, this enzyme was calcium-independent. The fact that TGase was capable to incorporate a wide variety of aliphatic and aromatic non-polar compounds suggested that the amine fixation site could be an hydrophobic pocket. S cinnamoneum CBS 683.68 TGase was synthesised as a protein precursor of 411 amino acid residues corresponding to a signal peptide of 81 amino acid residues and a mature TGase of 330 amino acid residues. Amino acid sequence analysis revealed that the S cinnamoneum CBS 683.68 TGase had little sequence homology with eukaryotic TGases, but shared high identity with the sequence of Streptoverticillium strain S-8112. In accordance with kinetics data, hydropathy analysis showed that the active site of the enzyme was in an hydrophobic environment as for eukaryotic TGases.

Production and secretion of proteins by streptomycetes

Streptomycetes produce a large number of extracellular enzymes as part of their saprophytic mode of life. Their ability to synthesize enzymes as products of their primary metabolism could lead to the production of many proteins of industrial importance. The development of high-yielding expression systems for both homologous and heterologous gene products is of considerable interest. In this article, we review the current knowledge on the various factors that affect the production and secretion of proteins by streptomycetes and try to evaluate the suitability of these bacteria for the large-scale production of proteins of industrial importance.

A taxonomic review of the genera Kitasatosporia and Streptoverticillium by analysis of ribosomal protein AT-L30

An analysis of the ribosomal AT-L30 proteins from 42 strains of 35 species belonging to the genera Streptomyces, Streptoverticillium, and Kitasatosporia and related genera revealed that all of the members of the genera Streptoverticillium and Kitasatosporia examined had the same sequence as Streptomyces exfoliatus or a highly homologous sequence and exhibited high levels of relatedness to Streptomyces lavendulae. These results strongly support the previous suggestion of Witt and Stackebrandt (D. Witt and E. Stackebrandt, Syst. Appl. Microbiol. 13:361-371, 1990) and Wellington et al. (E. M. H. Wellington, E. Stackebrandt, D. Sanders, J. Wolstrup, and N. O. G. Jorgensen, Int. J. Syst. Bacteriol. 42:156-160, 1992) that the genera Streptoverticillium and Kitasatosporia should be united with the genus Streptomyces on the basis of 16S rRNA data.

Chemical synthesis of the gene for microbial transglutaminase from Streptoverticillium and its expression in Escherichia coli

The gene coding for microbial transglutaminase (TGase) from Streptoverticillium, which consists of 331 amino acids, was chemically synthesized. The codons have been substituted for those mainly favored in yeast. Our strategy involved the construction of the TGase gene in five sections (54 oligomers) that contained unique restriction enzyme sites at both ends, which could readily be ligated to form the full-length product. The chemically synthesized gene was inserted downstream from the ompA signal peptide of the E. coli expression vector, pIN-III-ompA, which carries lpp and lac promotors. The resultant plasmid directed the expression of TGase, with the activity being secreted mainly into the periplasmic space of E. coli. The induced gene product was identical with native TGase in size and in immunological properties, though the enzyme activity was low.

Functional and evolutionary implications of a survey of various actinomycetes for homologues of two Streptomyces coelicolor sporulation genes

In Streptomyces coelicolor A3(2) the whiB and whiG genes are essential for sporulation, their deduced products being a possible transcriptional activator and an RNA polymerase sigma factor, respectively. In a survey of DNA from diverse actinomycetes by Southern blotting, all samples tested hybridized with whiB, but only those representing genera capable of producing sporulating aerial mycelium hybridized with whiG. It is postulated that whiB may play a more intimate role in hyphal fragmentation processes (including sporulation) than whiG. The whiB and whiG homologues (whiB-Stv and whiG-Stv) of Streptoverticillium griseocarneum were cloned and sequenced, and subjected to functional tests in S. coelicolor whiB and whiG mutants. The genes were closely similar, but not identical, to their S. coelicolor counterparts at the DNA and deduced protein levels, and both Stv. griseocarnum gene products could function well in S. coelicolor. However, studies with hybrid transcription units suggested that the promoter region of whiB-Stv is somewhat inefficient in S. coelicolor.

Classification of acidophilic, neutrotolerant and neutrophilic streptomycetes by nucleotide sequencing of 5S ribosomal RNA

Complete 5S ribosomal RNA sequences were obtained for four acidophilic actinomycetes, seven neutrophilic streptomycetes and a strain of Streptoverticillium baldaccii. All of the organisms contained RNAs belonging to the 120 nucleotide type. An evolutionary tree was generated after combining the test data with results from similar studies on representative Gram-positive bacteria. The acidophilic, neutrotolerant and neutrophilic actinomycetes were recovered in a distinct cluster that was equated with the genus Streptomyces. The sequence data support the view that the genera Chainia, Elytrosporangium, Kitasatoa and Microellobosporia should be considered as synonyms of the genus Streptomyces. The recovery of the Streptoverticillium baldaccii strain on the fringe of the Streptomyces cluster is also consistent with current trends in the taxonomy of these organisms. Further work is needed to determine the taxonomic status of the two streptomycete subgroups that comprised the streptomycete cluster.