Organization and nucleotide sequence analysis of a ribosomal RNA gene cluster from Streptomyces ambofaciens

Streptomyces spp. Strains as Potential Biological Control Agents against Verticillium Wilt of Olive

Verticillium wilt of olive (VWO) caused by Verticillium dahliae is considered a major olive (Olea europaea) disease in Mediterranean-type climate regions. The lack of effective chemical products against VWO makes it necessary to search for alternatives such as biological control. The main goal of this study was to evaluate the effect of six Streptomyces spp. strains as biological control agents (BCAs) against VWO. All of them were molecularly characterized by sequencing 16S or 23S rRNA genes and via phylogenetic analysis. Their effect was evaluated in vitro on the mycelial growth of V. dahliae (isolates V004 and V323) and on microsclerotia (MS) viability using naturally infested soils. Bioassays in olive plants inoculated with V. dahliae were also conducted to evaluate their effect against disease progress. In all the experiments, the reference BCAs Fusarium oxysporum FO12 and Aureobasidium pullulans AP08 were included for comparative purposes. The six strains were identified as Streptomyces spp., and they were considered as potential new species. All the BCAs, including Streptomyces strains, showed a significant effect on mycelial growth inhibition for both V. dahliae isolates compared to the positive control, with FO12 being the most effective, followed by AP08, while the Streptomyces spp. strains showed an intermediate effect. All the BCAs tested also showed a significant effect on the inhibition of germination of V. dahliae MS compared to the untreated control, with FO12 being the most effective treatment. Irrigation treatments with Streptomyces strain CBQ-EBa-21 or FO12 were significantly more effective in reducing disease severity and disease progress in olive plants inoculated with V. dahliae compared to the remaining treatments. This study represents the first approach to elucidating the potential effect of Streptomyces strains against VWO.

DNA Data Visualization (DDV): Software for Generating Web-Based Interfaces Supporting Navigation and Analysis of DNA Sequence Data of Entire Genomes

Data visualization methods are necessary during the exploration and analysis activities of an increasingly data-intensive scientific process. There are few existing visualization methods for raw nucleotide sequences of a whole genome or chromosome. Software for data visualization should allow the researchers to create accessible data visualization interfaces that can be exported and shared with others on the web. Herein, novel software developed for generating DNA data visualization interfaces is described. The software converts DNA data sets into images that are further processed as multi-scale images to be accessed through a web-based interface that supports zooming, panning and sequence fragment selection. Nucleotide composition frequencies and GC skew of a selected sequence segment can be obtained through the interface. The software was used to generate DNA data visualization of human and bacterial chromosomes. Examples of visually detectable features such as short and long direct repeats, long terminal repeats, mobile genetic elements, heterochromatic segments in microbial and human chromosomes, are presented. The software and its source code are available for download and further development. The visualization interfaces generated with the software allow for the immediate identification and observation of several types of sequence patterns in genomes of various sizes and origins. The visualization interfaces generated with the software are readily accessible through a web browser. This software is a useful research and teaching tool for genetics and structural genomics.

Taxonomic study of a salt tolerant Streptomyces sp. strain C-2012 and the effect of salt and ectoine on lon expression level

Streptomyces strain C-2012 is a salt tolerant biocontrol PGPR that has been isolated from Iranian soil. The main aim of current study was finding strain C-2012 taxonomic position and to find the genes which are potentially involved in salt tolerance phenotype. Strain C-2012 chemotaxonomic, morphological and molecular characteristics indicate that this strain is a member of the genus Streptomyces. Phylogenetic analyses based on an almost complete 16S rRNA gene sequence revealed that this strain is closely related to Streptomyces rimosus JCM 4667(T). Also, DNA-DNA hybridization test estimated 74% relatedness between two strains and confirmed that C-2012 is a strain of S. rimosus. In order to find novel genes that are differentially expressed in response to the salt treatment, cDNA-AFLP was carried out. One of the selected expressed sequence tags (TDF-1) was found to be homologous to lon gene which produces a bacterial ATP-dependent proteases (proteases LA). Lon gene expression was induced following 450 mM salt (NaCl) treatment and its expression level was further (5.2-fold) increased in response to salt when ectoine was added to the medium. These results suggest that two protein protection systems including ectoine and ATP-dependent proteases synergistically are related. NaCl stress also caused an enhancement in the activity of extracellular protease.

Characterization and phylogenetic analysis of cellulase producing Streptomyces noboritoensis SPKC1

A cellulase producing strain of Actinomycetes was isolated from soil samples which were collected from Southwest ghats, Kerala, India at a depth of 6-12 inches and Actinomycetes was characterized by morphological, cultural, physiological, chemotaxonomical and phylogenetic analysis. The 16S rRNA region of this strain was amplified and sequenced. The Neighbor-joining and Maximum Parsimony algorithm with topology tree of 16S rRNA was constructed. Based on results of observation and phylogenetic analysis, the strain SPKC1 was proved to belong to the species Streptomyces noboritoensis with cellulase activity. The Carboxy Methyl Cellulose (CMCase) activities of the strain SPKC1 on eighth day an amount of 910 microg/ml of glucose, 210 microg/ml of protein and 850 mg/100 ml of growth (biomass) on ninth day were recorded. In exocellulase activity strain SPKC1 on first day an amount of 500 microg/ml glucose was produced.

Localization and transmission route of Coriobacterium glomerans, the endosymbiont of pyrrhocorid bugs

Endosymbiotic gut bacteria play an essential role in the nutrition of many insects. Most of the nutritional interactions investigated so far involve gammaproteobacterial symbionts, whereas other groups have received comparatively little attention. Here, we report on the localization and the transmission route of the specific actinobacterial symbiont Coriobacterium glomerans from the gut of the red firebug, Pyrrhocoris apterus (Hemiptera: Pyrrhocoridae). The symbionts were detected by diagnostic PCRs and FISH in the midgut section M3, in the rectum and in feces of the bugs as well as in the hemolymph of some females. Furthermore, adult female bugs apply the symbionts to the surface of the eggs during oviposition, from where they are later taken up by the hatchlings. Surface sterilization of egg clutches generated aposymbiotic insects and thereby confirmed the vertical transmission route via the egg surface. However, symbionts were readily acquired horizontally when the nymphs were reared in the presence of symbiont-containing eggshells, feces, or adult bugs. Using diagnostic PCRs and partial sequencing of the 16S rRNA gene, closely related bacterial symbionts were detected in the cotton stainer bug Dysdercus fasciatus (Hemiptera: Pyrrhocoridae), suggesting that the symbiosis with Actinobacteria may be widespread among pyrrhocorid bugs.

Macrolide resistance

The macrolides have evolved through four chemical generations since erythromycin became available for clinical use in 1952. The first generation, the 14-membered ring macrolide erythromycin, induced resistance and was replaced by the second generation 16-membered ring macrolides which did not. The inability to induce came at the price of mutation, in the pathogenic target strain, to constitutive expression of resistance. A third generation of macrolides improved the acid-stability, and therefore the pharmacokinetics of erythromycin, extending the clinical use of macrolides to Helicobacter pylori and Mycobacterium tuberculosis. Improved pharmacokinetics resulted in the selection of intrinsically resistant mutant strains with rRNA structural alterations. Expression of resistance in these strains was unexpected, explainable by low rRNA gene copy number which made resistance dominant. A fourth generation of macrolides, the 14-membered ring ketolides are the most recent development. Members of this generation are reported to be effective against inducibly resistant strains, and ketolide resistant strains have not yet been reported. In this review we discuss details of the ways in which bacteria have become resistant to the first three generations of macrolides, both with respect to their biochemistry, and the genetic mechanisms by which their expression is regulated.

Non-specific association between filamentous bacteria and fungus-growing ants

Fungus-growing ants and their fungal cultivar form a highly evolved mutualism that is negatively affected by the specialized parasitic fungus Escovopsis. Filamentous Pseudonocardia bacteria occurring on the cuticle of attine ants have been proposed to form a mutualistic interaction with these ants in which they are vertically transmitted (i.e. from parent to offspring colonies). Given a strictly vertical transmission of Pseudonocardia, the evolutionary theory predicts a reduced genetic variability of symbionts among ant lineages. The aim of this study was to verify whether actinomycetes, which occur on Acromyrmex octospinosus leaf-cutting ants, meet this expectation by comparing their genotypic variability with restriction fragment length polymorphisms. Multiple actinomycete strains could be isolated from both individual ant workers and colonies (one to seven strains per colony). The colony specificity of actinomycete communities was high: Only 15% of all strains were isolated from more than one colony, and just 5% were present in both populations investigated. Partial sequencing of 16S ribosomal deoxyribonucleic acid of two of the isolated strains assigned both of them to the genus Streptomyces. Actinomycetes could also be isolated from workers of the two non-attine ant species Myrmica rugulosa and Lasius flavus. Sixty-two percent of the strains derived from attine ants and 80% of the strains isolated from non-attine ants inhibited the growth of Escovopsis. Our data suggest that the association between attine ants and their actinomycete symbionts is less specific then previously thought. Soil-dwelling actinomycetes may have been dynamically recruited from the environment (horizontal transmission), probably reflecting an adaptation to a diverse community of microbial pathogens.

Genetics of Streptomyces rimosus, the oxytetracycline producer

From a genetic standpoint, Streptomyces rimosus is arguably the best-characterized industrial streptomycete as the producer of oxytetracycline and other tetracycline antibiotics. Although resistance to these antibiotics has reduced their clinical use in recent years, tetracyclines have an increasing role in the treatment of emerging infections and noninfective diseases. Procedures for in vivo and in vitro genetic manipulations in S. rimosus have been developed since the 1950s and applied to study the genetic instability of S. rimosus strains and for the molecular cloning and characterization of genes involved in oxytetracycline biosynthesis. Recent advances in the methodology of genome sequencing bring the realistic prospect of obtaining the genome sequence of S. rimosus in the near term.

'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.

A new genus of the family Micromonosporaceae, Polymorphospora gen. nov., with description of Polymorphospora rubra sp. nov

Two actinomycete strains were isolated from soil surrounding mangrove roots. The isolates formed short spore chains with spores showing diverse shapes. The isolates contained glutamic acid, glycine, alanine and meso-diaminopimelic acid in the cell wall, 3-O-methylmannose, mannose, galactose and glucose as the whole-cell sugars and MK-10(H6), MK-10(H4), MK-9(H6) and MK-9(H4) as the predominant isoprenoid quinones. The isolates formed a distinct taxon in the phylogenetic tree of the Micromonosporaceae based on analysis of 16S rRNA gene sequences and showed chemical and phenotypic properties that were different from members of all of the other genera of this family. Based on these observations, it is proposed that the novel isolates belong to a new genus, Polymorphospora gen. nov. The type species of the genus is proposed as Polymorphospora rubra sp. nov., with strain TT 97-42T (=NBRC 101157T=DSM 44947T) as the type strain.

Amplification of DNA encoding entire type I polyketide synthase domains and linkers from streptomyces species

Polyketides are a group of bioactive compounds from bacteria, plants, and fungi. To increase the availability of analogs for testing, the active sites of polyketide synthases are often substituted with homologous domains having altered substrate specificities. This study reports the design of polymerase chain reaction primers that enables isolation of entire active site domains from type I polyketide synthases with native interdomain linkers. This bypasses the need for further genetic screening to obtain functional units for use in genetic engineering. This is especially important in bioprospecting projects exploring new environments for bioresources.

Characterization of Streptomyces MITKK-103, a newly isolated actinomycin X2-producer

A new actinomycete strain designated MITKK-103 was isolated from the soil of a flowerpot using a humic acid agar medium. The newly isolated strain was able to produce a large amount of actinomycin X2 even under nonoptimized growing conditions and serves as a promising source of this antibiotic. Actinomycin X2 has higher cytotoxicity toward cultured human leukemia (HL-60) cells than does actinomycin D, and it induces cell death via apoptosis. A nearly complete 16S ribosomal DNA (rDNA) sequence from the isolate was determined and found to have high identity (98.5-100%) with Streptomyces galbus, Streptomyces griseofuscus, and Streptomyces padanus, indicating that MITKK-103 belongs to the genus Streptomyces. The isolate clustered with species belonging to the S. padanus clade in a 16S-rDNA-based phylogenetic tree and showed 75% overall homology to S. padanus ATCC 25646 in DNA-DNA relatedness analysis. Although the growth of the isolate was somewhat different from the three species mentioned, the strain MITKK-103 most closely resembles S. padanus on the basis of the morphological and phenotypic characteristics, phylogenetic analysis, and genotypic data. As such, this is the first report of a strain of S. padanus capable of producing actinomycins.

Symbiotic bacteria protect wasp larvae from fungal infestation

Symbiotic associations between different organisms are of great importance for evolutionary and ecological processes [1-4]. Bacteria are particularly valuable symbiotic partners owing to their huge diversity of biochemical pathways that may open entirely new ecological niches for higher organisms [1-3]. Here, we report on a unique association between a new Streptomyces species and a solitary hunting wasp, the European beewolf (Philanthus triangulum, Hymenoptera, Crabronidae). Beewolf females cultivate the Streptomyces bacteria in specialized antennal glands and apply them to the brood cell prior to oviposition. The bacteria are taken up by the larva and occur on the walls of the cocoon. Bioassays indicate that the streptomycetes protect the cocoon from fungal infestation and significantly enhance the survival probability of the larva, possibly by producing antibiotics. Behavioral observations strongly suggest a vertical transmission of the bacteria. Two congeneric beewolf species harbor closely related streptomycetes in their antennae, indicating that the association with protective bacteria is widespread among philanthine wasps and might play an important role in other insects as well. This is the first report on the cultivation of bacteria in insect antennae and the first case of a symbiosis involving bacteria of the important antibiotic-producing genus Streptomyces.

Variation in 16S-23S rRNA intergenic spacer regions in Photobacterium damselae: a mosaic-like structure

Phenotypically, Photobacterium damselae subsp. piscicida and P. damselae subsp. damselae are easily distinguished. However, their 16S rRNA gene sequences are identical, and attempts to discriminate these two subspecies by molecular tools are hampered by their high level of DNA-DNA similarity. The 16S-23S rRNA internal transcribed spacers (ITS) were sequenced in two strains of Photobacterium damselae subsp. piscicida and two strains of P. damselae subsp. damselae to determine the level of molecular diversity in this DNA region. A total of 17 different ITS variants, ranging from 803 to 296 bp were found, some of which were subspecies or strain specific. The largest ITS contained four tRNA genes (tDNAs) coding for tRNA(Glu(UUC)), tRNA(Lys(UUU)), tRNA(Val(UAC)), and tRNA(Ala(GGC)). Five amplicons contained tRNA(Glu(UUC)) combined with two additional tRNA genes, including tRNA(Lys(UUU)), tRNA(Val(UAC)), or tRNA(Ala(UGC)). Five amplicons contained tRNA(Ile(GAU)) and tRNA(Ala(UGC)). Two amplicons contained tRNA(Glu(UUC)) and tRNA(Ala(UGC)). Two different isoacceptor tRNA(Ala) genes (GGC and UGC anticodons) were found. The five smallest amplicons contained no tRNA genes. The tRNA-gene combinations tRNA(Glu(UUC))-tRNA(Val(UAC))-tRNA(Ala(UGC)) and tRNA(Glu(UUC))-tRNA(Ala(UGC)) have not been previously reported in bacterial ITS regions. The number of copies of the ribosomal operon (rrn) in the P. damselae chromosome ranged from at least 9 to 12. For ITS variants coexisting in two strains of different subspecies or in strains of the same subspecies, nucleotide substitution percentages ranged from 0 to 2%. The main source of variation between ITS variants was due to different combinations of DNA sequence blocks, constituting a mosaic-like structure.

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.

Streptomyces speibonae sp. nov., a novel streptomycete with blue substrate mycelium isolated from South African soil

An actinomycete with blue substrate mycelium was isolated from a soil sample in Cape Town, South Africa, and designated strain PK-Blue(T). The colour of the substrate mycelium was not sensitive to changes in pH. The organism produced hairy spores in Spirales-type spore chains. Chemical taxonomy indicated that it belonged to the genus Streptomyces. Strain PK-Blue(T) produced no diffusible pigments other than melanin, grew at 45 degrees C, did not degrade adenine and exhibited no antibacterial activity against Enterococcus faecium, Escherichia coli or Pseudomonas aeruginosa. Analysis of its 16S rRNA gene sequence and the results of physiological tests showed that strain PK-Blue(T) (= DSM 41797(T) = ATCC BAA-411(T)) represents the type strain of a novel species of Streptomyces, for which the name Streptomyces speibonae sp. nov. is proposed.

Diversity of streptomycetes in water-damaged building materials based on 16S rDNA sequences

AIMS

The diversity of streptomycetes in two different types of water-damaged building materials was investigated.

METHODS AND RESULTS

Direct PCR amplification of 16S rDNA from DNA isolated from building materials, cloning of the fragments and sequence analysis were used. In the phylogenetic analysis of the variable gamma region of the PCR amplification products, the sequences affiliated with five groups.

CONCLUSIONS

Several different sequences were found in both materials, suggesting the presence of several species. Also, previously unknown sequences were detected, although all the sequences clustered together with sequences of known species.

SIGNIFICANCE AND IMPACT OF THE STUDY

Streptomycetes are known as indicators for moisture and mould damage in buildings and potential health risk, but their diversity in indoor environments is still unknown.

Intragenomic and intraspecific polymorphism of the 16S-23S rDNA internally transcribed sequences of Streptomyces ambofaciens

The nucleotide composition of the internally transcribed sequences (ITSs) of the six rDNA operons of two strains of Streptomyces ambofaciens were determined. Four variable and five conserved nucleotide blocks were distinguished. Five different modular organizations were revealed for each strain and no homologous loci showed the same succession of blocks. This suggests that recombination frequently occurs between the rDNA loci, leading to the exchange of nucleotide blocks. The modular structure was also observed within the ITSs of Streptomyces coelicolor M145, which is closely related to Streptomyces ambofaciens, and Streptomyces griseus 2247, showing the same number of constant blocks but with fewer variable regions. This confirms that a high degree of ITS variability is a common characteristic among Streptomyces spp. The functional significance of the combinations of variable and constant nucleotide blocks of the ITS was examined by in silico prediction of secondary structures from nucleotide sequences. The secondary structures were shown to be analogous whatever the combination of variable/constant blocks at the intragenomic, intraspecific and interspecific levels.

Horizontal transfer of the plant virulence gene, nec1, and flanking sequences among genetically distinct Streptomyces strains in the Diastatochromogenes cluster

Evidence for the horizontal transfer of a pathogenicity island (PAI) carrying the virulence gene nec1 and flanking sequences among Streptomyces strains in the Diastatochromogenes cluster is presented. Plant-pathogenic, thaxtomin-producing Streptomyces strains, previously classified as S. scabiei based on the conventionally used phenotypic characteristics, were found to be genetically distinct from the type strain of S. scabiei based on DNA relatedness and 16S rDNA sequence analysis. Pairwise DNA-DNA hybridizations between some of these strains and the S. scabiei type strain were as low as 36%, a value much below what is conventionally accepted for species identity (70%). The sequence of the nec1 gene, however, was identical in all the S. scabiei and S. scabiei-like strains tested, irrespective of their DNA relatedness to the type strain of S. scabiei, their geographic origin, or the isolation host. Furthermore, a 26-kb DNA fragment including and flanking nec1 was also conserved among these strains based on restriction and Southern analyses. These data indicate that the etiology of potato scab is more complex than previously recognized; this result has important implications for potato scab management strategies. Previous research has suggested that horizontal transfer of a PAI was the mechanism for evolution of pathogenicity in S. acidiscabies and S. turgidiscabies, species that lie outside of the Diastatochromogenes cluster. Data presented here support this model and indicate that PAI transfer also has occurred frequently in species closely related to S. scabiei.

PCR primers targeting the 16S rRNA gene for the specific detection of streptomycetes

Streptomycetes are filamentous actinobacteria commonly found in soil and biotechnically important, but they also have adverse effects on human health. In this work, two primer pairs, StrepB/StrepE and StrepB/StrepF combined with Bst YI restriction endonuclease digestion, targeting the 16S rRNA gene of streptomycetes were designed. The specificity of the primers was determined by polymerase chain reaction (PCR) amplification from Streptomyces strains and near relatives. All streptomycetes tested positive and non-streptomycetes were not amplified except three strains that, however, gave Bst YI restriction endonuclease digestion results distinct from streptomycetes. Moreover, both primer pairs gave an amplification product of the expected size only when Streptomyces VTT E-99-1334 DNA was present in the template DNA mixture isolated from six bacterial and three fungal strains. The primers were further successfully used to amplify from DNA isolated from two soil and two building material samples. The 40 sequenced amplification products obtained with the primer pair StrepB/StrepE showed greater than 96.1% similarity to streptomycete 16S rRNA sequences. Seventy PCR amplification products obtained with the primers StrepB/StrepF were analysed by sequencing and restriction analysis. All 54 PCR products having >95.7% similarity to streptomycete sequences were cleaved with Bst YI. No false-positive results were achieved. Both primer sets proved to be specific for streptomycetes, and applicable for the detection of streptomycetes in environmental samples.

Is the 16S-23S rRNA internal transcribed spacer region a good tool for use in molecular systematics and population genetics? A case study in cyanobacteria

We amplified, TA-cloned, and sequenced the 16S-23S internal transcribed spacer (ITS) regions from single isolates of several cyanobacterial species, Calothrix parietina, Scytonema hyalinum, Coelodesmium wrangelii, Tolypothrix distorta, and a putative new genus (isolates SRS6 and SRS70), to investigate the potential of this DNA sequence for phylogenetic and population genetic studies. All isolates carried ITS regions containing the sequences coding for two tRNA molecules (tRNA and tRNA). We retrieved additional sequences without tRNA features from both C. parietina and S. hyalinum. Furthermore, in S. hyalinum, we found two of these non-tRNA-encoding regions to be identical in length but different in sequence. This is the first report of ITS regions from a single cyanobacterial isolate not only different in configuration, but also, within one configuration, different in sequence. The potential of the ITS region as a tool for studying molecular systematics and population genetics is significant, but the presence of multiple nonidentical rRNA operons poses problems. Multiple nonidentical rRNA operons may impact both studies that depend on comparisons of phylogenetically homologous sequences and those that employ restriction enzyme digests of PCR products. We review current knowledge of the numbers and kinds of 16S-23S ITS regions present across bacterial groups and plastids, and we discuss broad patterns congruent with higher-level systematics of prokaryotes.

Mycobacterium avium subsp. paratuberculosis in Veterinary Medicine

Mycobacterium avium subsp. paratuberculosis (basonym M. paratuberculosis) is the etiologic agent of a severe gastroenteritis in ruminants known as Johne's disease. Economic losses to the cattle industry in the United States are staggering, reaching $1.5 billion annually. A potential pathogenic role in humans in the etiology of Crohn's disease is under investigation. In this article, we review the epidemiology, pathogenesis, diagnostics, and disease control measures of this important veterinary pathogen. We emphasize molecular genetic aspects including the description of markers used for strain identification, diagnostics, and phylogenetic analysis. Recent important advances in the development of animal models and genetic systems to study M. paratuberculosis virulence determinants are also discussed. We conclude with proposals for the applications of these models and recombinant technology to the development of diagnostic, control, and therapeutic measures.

Organization, structure, and variability of the rRNA operon of the Whipple's disease bacterium (Tropheryma whippelii)

Whipple's disease is a systemic disorder associated with a cultivation-resistant, poorly characterized actinomycete, Tropheryma whippelii. We determined a nearly complete rRNA operon sequence of T. whippelii from specimens from 3 patients with Whipple's disease, as well as partial operon sequences from 43 patients. Variability was observed in the 16S-23S rRNA spacer sequences, leading to the description of five distinct sequence types. One specimen contained two spacer sequence types, raising the possibility of a double infection. Secondary structure models for the primary rRNA transcript and mature rRNAs revealed rare or unique features.

Characterization of the ribosomal rrnD operon of the cephamycin-producer 'Nocardia lactamdurans' shows that this actinomycete belongs to the genus Amycolatopsis

The cephamycin producer strain 'Nocardia lactamdurans' contains four ribosomal RNA (rrn) operons. One of them (rrnD) was cloned from a DNA library in the bifunctional cosmid pJAR4. A 2229 bp region of rrnD has been sequenced. The 'N. lactamdurans' rrnD operon maintains the canonical order 5'-16S-23S-5S-3'. Four of the consensus Gürtler-Stanisch sequences were found in the 16S rRNA gene and a fifth one in the sequenced 5' region of the 23S rRNA gene. The anti Shine-Dalgarno sequence of 'N. lactamdurans' (located in the 3'-end of the 16S rRNA gene) was found to be 5'-CCUCCUUUCU-3' and is identical to that of Corynebacterium lactofermentum and Mycobacterium tuberculosis. A phylogenetic analysis of 'N. lactamdurans' by the neighbor-joining method using the entire 16S rRNA nucleotide sequence revealed that this actinomycete is closely related to Amlycolatopsis orientalis subsp orientalis, Amycolatopsis coloradensis, Amycolatopsis alba, Amycolatopsis sulphurea and other Amycolatopsis sp. but only distantly related to species of the genus Nocardia. The cephamycin producer 'N. lactamdurans' NRRL 3802 should be, therefore, classified as Amycolatopsis lactamdurans. The deduced secondary structure of the 16S rRNA is very similar to that of A. colorandensis and A. alba but different from those of species of the Nocardia genus supporting the incorporation of 'N. lactamdurans' into the genus Amycolatopsis.

Phylogenetic Analysis of 16S rRNA Genes and PCR Analysis of the nec1 Gene from Streptomyces spp. Causing Common Scab, Pitted Scab, and Netted Scab in Finland

ABSTRACT The sequences of the 16S rRNA genes (nucleotides 29 to 1,521) from various Streptomyces strains pathogenic to potato were compared. These included 10 pathogenic Streptomyces strains isolated from potato scab lesions in Finland, the type strains of S. aureofaciens NRRL 2209(T) and S. lydicus ATCC 25470(T), 'S. griseus subsp. scabies' ATCC 10246, and two S. griseus strains that were originally deposited to the collection as pathogens. The nucleotide sequence (>94.5% sequence identity [SI]) and length (1,469 to 1,481 nucleotides) of the analyzed region varied. Phylogenetic analysis of 16S rRNA genes placed Finnish strains into three species, supported by previously characterized morphological and physiological traits. Six Finnish strains, including two strains that deviated from the others in one trait (no spiral sporophores or D-xylose utilization), had identical 16S rRNA genes and were identified as S. scabies (99.9% SI to S. scabies ATCC 49173). Three Finnish strains were identified as S. turgidiscabies, a species previously described only in Japan (99.9% SI to S. turgidiscabies ATCC 700248). Finnish strain 317 and S. aureofaciens NRRL 2209 (99.8% SI) were placed in a distinct phylogenetic cluster together with Kitosatospora spp., which suggests that S. aureofaciens may belong to the recently revived genus Kitosatospora. In pathogenicity tests, S. scabies caused characteristic symptoms of common scab, S. turgidiscabies caused mainly pitted scab, and S. aureofaciens caused netted scab and necrotic lesions on stolons of potato cultivars Bintje and Matilda in the greenhouse. The nec1 gene and the intergenic region between nec1 and the 5' transposase pseudogene ORFtnp were successfully amplified by polymerase chain reaction from S. scabies ATCC 49173 and the pathogenic Finnish strains of S. scabies, but not from a nonpathogenic strain of S. scabies, three pathogenic and two nonpathogenic strains of S. turgidiscabies, and S. aureofaciens.

Molecular cloning and comparative sequence analyses of rRNA operons in Streptomyces nodosus ATCC 14899

The genome of Streptomyces nodosus contains six ribosomal RNA (rRNA) operons. Four of the rRNA operons; rrnB, rrnD, rrnE and rrnF were cloned. We have completely sequenced all four operons, including a region 750 base pairs (bp) upstream of the 16S rRNA gene. The three rRNA genes present in each operon were closely linked in the order 16S-23S-5S. A sequence comparison of the four operons showed more than 99% sequence similarity between the corresponding 16S and 23S rRNA genes, and more than 97% similarity between 5S rRNA genes. The sequence differences observed between 23S rRNA genes appeared to be localized in two specific regions. Substantial sequence differences were found in the region upstream of the 16S rRNA gene as well as in the internal transcribed spacers. No tRNA gene was found in the 16S-23S spacer regions.

Two distinct mechanisms cause heterogeneity of 16S rRNA

To investigate the frequency of heterogeneity among the multiple 16S rRNA genes within a single microorganism, we determined directly the 120-bp nucleotide sequences containing the hypervariable alpha region of the 16S rRNA gene from 475 Streptomyces strains. Display of the direct sequencing patterns revealed the existence of 136 heterogeneous loci among a total of 33 strains. The heterogeneous loci were detected only in the stem region designated helix 10. All of the substitutions conserved the relevant secondary structure. The 33 strains were divided into two groups: one group, including 22 strains, had less than two heterogeneous bases; the other group, including 11 strains, had five or more heterogeneous bases. The two groups were different in their combinations of heterogeneous bases. The former mainly contained transitional substitutions, and the latter was mainly composed of transversional substitutions, suggesting that at least two mechanisms, possibly misincorporation during DNA replication and horizontal gene transfer, cause rRNA heterogeneity.

Diversity of frankia strains in root nodules of plants from the families elaeagnaceae and rhamnaceae

Partial 16S ribosomal DNAs (rDNAs) were PCR amplified and sequenced from Frankia strains living in root nodules of plants belonging to the families Elaeagnaceae and Rhamnaceae, including Colletia hystrix, Elaeagnus angustifolia, an unidentified Elaeagnus sp., Talguenea quinquenervia, and Trevoa trinervis. Nearly full-length 16S rDNAs were sequenced from strains of Frankia living in nodules of Ceanothus americanus, C. hystrix, Coriaria arborea, and Trevoa trinervis. Partial sequences also were obtained from Frankia strains isolated and cultured from the nodules of C. hystrix, Discaria serratifolia, D. trinervis, Retanilla ephedra, T. quinquenervia, and T. trinervis (Rhamnaceae). Comparison of these sequences and other published sequences of Frankia 16S rDNA reveals that the microsymbionts and isolated strains from the two plant families form a distinct phylogenetic clade, except for those from C. americanus. All sequences in the clade have a common 2-base deletion compared with other Frankia strains. Sequences from C. americanus nodules lack the deletion and cluster with Frankia strains infecting plants of the family Rosaceae. Published plant phylogenies (based on chloroplast rbcL sequences) group the members of the families Elaeagnaceae and Rhamnaceae together in the same clade. Thus, with the exception of C. americanus, actinorhizal plants of these families and their Frankia microsymbionts share a common symbiotic origin.

Expression of the Streptomyces aureofaciens glyceraldehyde-3-phosphate dehydrogenase gene (gap) is developmentally regulated and induced by glucose

In previous experiments, the Streptomyces aureofaciens gap gene encoding glyceraldehyde-3-phosphate dehydrogenase (GAPDH) was identified. To investigate expression of the gene, S1 nuclease mapping and Northern blot hybridization were performed using RNA prepared from S. aureofaciens cultivated under various conditions. These studies suggested monocistronic organization and developmental regulation of the gene. A single promoter, gap-P, was identified upstream of the gap coding region. In cultures grown on solid medium in the absence of glucose, its transcription was induced at the time of aerial mycelium formation. In addition, gap transcription was also induced in substrate mycelium by glucose. A promoter-bearing DNA fragment was inserted into two promoter-probe vectors, to give expression patterns consistent with the results of direct RNA analysis.

Ribosomal RNA synthesis in Streptomyces lividans under heat shock conditions

Clones containing rRNA genes were isolated from a gene library of Streptomyces lividans when RNA produced under heat shock conditions was used as a probe. Two of the clones carried entire rRNA operons rrnA and rrnF, respectively, the expression of both operons being under the control of four different promoters. At least two of the promoters were fully functional when the temperature increased from 30 to 45 degrees C, ensuring transcription of the rRNA genes under the heat shock. A third clone carried a partial rRNA operon in which expression was controlled by a main promoter that was functional at both 30 and 45 degrees C.

Application of the variable region in 16S rDNA to create an index for rapid species identification in the genus Streptomyces

Partial nucleotide sequences (120 bp) of the 16S rRNA gene (rDNA) containing a variable alpha region were compared in 89 strains of the genus Streptomyces belonging to eight major clusters of category I in Bergey's Manual of Systematic Bacteriology. Fifty-seven kinds of partial 16S rDNA sequences were observed among the 89 strains. Forty-three of the strains were grouped into 11 'identity groups', based on the fact that the strains in each group shared an identical sequence in the 120-bp region. The results of a phylogenetic analysis based on the 16S rDNA 120-bp sequences revealed that 60 of the 89 strains could be categorized into seven clusters, each consisting of four or more strains. Based on these observations it was concluded that short nucleotide sequences bearing the variable alpha region are useful for Streptomyces species identification.

Primary and secondary structures of rRNA spacer regions in enterococci

The 16S-23S and 23S-5S rRNA spacer DNA regions (spacer regions 1 and 2, respectively) from Enterococcus faecalis, Enterococcus faecium, Enterococcus hirae, Enterococcus durans and Enterococcus mundtii were amplified by PCR. Their nucleotide sequences were established and a secondary structure model showing the interaction between the two spacer regions was built. Whereas lactococci and Streptococcus sensu stricto are characterized by a single type of spacer region 1, the enterococci show a high degree of variability in this region; thus the spacer regions 1 with and without tRNA(Ala) were characterized. However, as shown for lactococci and Streptococcus sensu stricto, the tRNA(Ala) gene does not encode the 3'-terminal CCA trinucleotide. A putative antitermination signal is found downstream from the tRNA(Ala) gene. Based on comparison with Lactococcus lactis and Streptococcus thermophilus, a double-stranded processing stem is proposed. In E, hirae, one of the three different types of spacer region 1 contains no tRNA(Ala), but displays a 107 nt insertion that forms a long stem-loop structure. A similar insertion (115 nt in length) was found in E. faecium and base compensatory mutations preserve the ability to form the long stem-loop structure. Such insertions may correspond to mobile intervening sequences, as found in the 23S rRNA coding sequences of some Gram-negative bacteria. The spacer regions 1 and 2 from the three subgroups of streptococci were compared, and except for the tRNA(Ala) gene and the double-stranded processing sites, little similarity was found, which opens large possibilities for future development of DNA-based typing methods.

Organization and nucleotide sequence analysis of the ribosomal gene set (rrnB) from Streptomyces lividans

Streptomyces lividans (Sl) contains six ribosomal RNA (rRNA) gene sets, rrnA-F (Suzuki, Y., Ono, Y., Nagata, A. and Yamada, T. (1988) Molecular cloning and characterization of an rRNA operon in Streptomyces lividans TK21. J. Bacteriol. 170, 1631-1636). We have cloned the rrnB gene cluster. Physical mapping revealed that rrnB gene set is located on a 290 kb Asel fragment in the 11 to 12 o'clock region of the S. coelicolor A3(2) chromosome. The complete nucleotide (nt) sequence of Sl 23S rRNA has been determined. The structural gene of the Sl 23S rRNA codes for the 3108 nt RNA chain. The G+C content of the 23S rRNA is 57.3 mol%. The length of the spacer region between the 23S and 5S genes is 99 bp. Analysis of the sequences between the 16S and 23S genes and downstream of the 5S rRNA gene failed to identify any tRNA-like sequences. A secondary structure model of Sl 23 rRNA is proposed, based on the earlier published model of Gutell and Fox (Nucleic Acids Res. 16 (1988) 175-269).

Mapping of the ribosomal operons on the linear chromosomal DNA of Streptomyces ambofaciens DSM40697

Streptomyces ambofaciens DSM40697 possess six rRNA gene clusters which can be distinguished by probing BfrI-digested total DNA with the PCR-amplified l6S-23S ribosomal genet internal transcribed spacer. The six rrn loci of S. ambofaciens were cloned as recombinant cosmids and located on the AseI-Dŕal physical map of the linear chromosomal DNA. For five of the six ribosomal gene sets, the transcriptional orientation was determined relative to the physical map and was shown to be divergent away from an oriC-like locus.

Analysis of partial sequences of genes coding for 16S rRNA of actinomycetes isolated from Casuarina equisetifolia nodules in Mexico

Filamentous bacteria isolated from surface-sterilized nodules of Casuarina equisetifolia trees in México were capable of reducing acetylene, a diagnostic test for nitrogenase, but were unable to nodulate their host. Analysis of partial 16S rRNA gene sequences suggests that the Mexican isolates are not Frankia strains but members of a novel clade.

Characterization of Streptomyces venezuelae ATCC 10595 rRNA gene clusters and cloning of rrnA

Streptomyces venezuelae ATCC 10595 harbors seven rRNA gene clusters which can be distinguished by BglII digestion. The three rRNA genes present in each set are closely linked with the general structure 16S-23S-5S. We cloned rrnA and sequenced the 16S-23S spacer region and the region downstream of the 5S rRNA gene. No tRNA gene was found in these regions.

Determination of 16S ribosomal RNA gene copy number in Streptococcus uberis, S. agalactiae, S. dysgalactiae and S. parauberis

Species-specific oligonucleotide probes and a universal oligonucleotide probe derived from sequences of 16S rRNA were hybridised to chromosomal DNA from Streptococcus agalactiae, S. dysgalactiae, S. parauberis and S. uberis following digestion with EcoRI. Due to the presence of a unique EcoRI site in each 16S rRNA gene, the number of hybridised fragments was indicative of the number of 16S rRNA genes. Southern hybridisation indicated six 16S rRNA genes in ten isolates of S. agalactiae, five genes in ten isolates of S. uberis, five genes in six isolates and six in another isolate of S. dysgalactiae, and six genes in four isolates of S. parauberis. For a fifth isolate of S. parauberis, six 16S rRNA genes were indicated by the universal probe but only five when hybridised to the species-specific probe, indicating sequence variation (microheterogeneity) within the probe target region.

Rho-independent terminators without 3' poly-U tails from the early region of actinophage øC31

Previous work has identified three intergenic regions from the early region of actinophage øC31 where transcription was either terminated or the mRNA was processed. Here we show using in vivo and in vitro approaches that these regions contain rho-independent terminators designated eta, etb and etc. Transcripts through eta-c would be expected to form stable RNA stem-loops but would lack poly-U tails. Eta-c contained part or all of the conserved sequences 5' AGCCCC and 5' GGGGCTT. A Streptomyces 'terminator probe' vector, pUGT1, was constructed and used to assay the efficiency of termination of transcription by eta-c from the thiostrepton-inducible tipA promoter by measuring the expression of a downstream reporter gene (aphII). In pUGT1 etb was at best a minor terminator in vivo whilst eta and etc exhibited strong termination activity. In vitro termination was assayed using templates containing a synthetic promoter recognised by E.coli RNA polymerase and fragments containing eta-c inserted downstream. All three terminators stimulated the formation of 3' ends in the promoter-distal arm of the inverted repeats with efficiencies eta > etc > etb. As all three terminators either overlap with or lie close to sequences which interact with phage repressor proteins (conserved inverted repeats, CIRs) and these can potentially form stem-loop structures in RNA, the effect of CIRs on termination was also investigated. Termination at etb was unaffected by the presence or absence on the transcription template of CIR3. CIR4 forms the central 17 bp of etc and a 37 nt deletion which eliminated this stem-loop abolished termination in vivo and in vitro. Eta was investigated using an antisense oligonucleotide interference assay; an oligo designed to bind the 5' arm of eta inhibited termination whilst an oligo antisense to CIR5 was ineffective and an oligo targeted further upstream enhanced termination. Taken together these data show that eta-c are intrinsic, rho-independent terminators of varying efficiencies despite the absence of a poly-U tail.

rRNA operon restriction derived taxa for Streptomyces (RiDiTS)

A method for grouping Streptomyces strains by fingerprints of their rRNA operons is described. In polyacrylamide gels, multicopy rRNA operon fragments in Streptomyces genomic MseI fingerprints produced intense bands which are well resolved from the less conspicuous low copy fragments interspersed between them. The high intensity multicopy rRNA bands are easily distinguished from the low intensity bands, eliminating the need for Southern blot hybridization to visualize the rRNA fragments. Direct evidence that the high-intensity bands in these polyacrylamide gels originated from rRNA operons was provided by a 'differential' Southern blot technique. We have used this method to assign 98 strains to 11 rRNA fingerprint type groups. This clustering method may be applicable to any prokaryote with a high G+C content genome.

Molecular relationship of an atypical Azospirillum strain 4T to other Azospirillum species

DNA/DNA hybridization, plasmid content and partial 16S rDNA sequence were determined to confirm the relationship between two Azospirillum strains, 4B and 4T, isolated from the same rice rhizosphere. The partial 16S rDNA sequence was determined for 9 strains belonging to 5 Azospirillum species which included Azospirillum lipoferum strains 4B and 4T, and was compared to a set of ribosomal sequences from other bacteria of the alpha subdivision of the Proteobacteria. Four Azospirillum species sequences were found to form a coherent group, whereas A. halopraeferens was found to be more divergent. The five Azospirillum species were closely related to Magnetospirillum and to a lesser extent to Rhodospirillum, with which they share some morphological features. The partial 16S rDNA sequences of the two strains 4B and 4T were identical and confirmed the closeness of these two strains. Plasmid content and DNA/DNA hybridization data (S1 nuclease and delta Tm) grouped Azospirillum strains 4B and 4T with the other strains of species Azospirillum lipoferum (USA5a, 59b, BR17). Other biochemical and genetic characters confirmed the grouping of Azospirillum strains 4B and 4T together with A. lipoferum.

tRNA genes of Streptomyces lividans: new sequences and comparison of structure and organization with those of other bacteria

Three closely linked Streptomyces lividans tRNA genes encoding two tRNA(Lys)s and a tRNA(Gly) were cloned and sequences. The structure of tRNA(Gly) is unusual for eubacterial tRNAs. Including those in previous reports (R. Sedlmeier and H. Schmieger, Nucleic Acids Res. 18:4027, 1990, and R. Sedlmeier, G. Linti, K. Gregor, and H. Schmieger, Gene 132:125-130, 1993), 18 S. lividans tRNA genes were physically mapped on the chromosome of the closely related strain Streptomyces coelicolor A3(2). The structure and organization of tRNA genes of S. lividans and S. coelicolor are compared with those of Escherichia coli and Bacillus subtilis.