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Journal Article

Studies on a strain of Kitasatospora sp. paclitaxel producer

TL;DR: The strain P&U 22869, which produces paclitaxel and related taxanes, discovered during the course of endophytic actinomycetes screening on Taxus baccata plants, was classified as Kitasatospora sp.
Abstract: The strain P&U 22869, which produces paclitaxel and related taxanes, discovered during the course of endophytic actinomycetes screening on Taxus baccata plants, was classified as Kitasatospora sp. on the basis of its morphological characteristics observed by light and scanning electron microscopy, the presence of the major constituents of its cell wall and the 16S rDNA sequence. The morphophysiological profile of the strain was compared with those of the valid and invalid species described for this genus. The paclitaxel production detected by means of monoclonal antibody assay (CIEA) was confirmed by LC-MS analysis and its concentration determined by HPLC. The de novo paclitaxel biosynthesis operated by strain P&U 22869 was demonstrated by biosynthesis experiments with labeled precursors.
Citations
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Journal ArticleDOI
TL;DR: New findings in the isolation methods, bio- and chemical diversity of endophytic actinobacteria are focused on and the potential biotechnological application is revealed.
Abstract: Endophytic actinobacteria, which exist in the inner tissues of living plants, have attracted increasing attention among taxonomists, ecologists, agronomists, chemists and evolutionary biologists. Numerous studies have indicated that these prolific actinobacteria appear to have a capacity to produce an impressive array of secondary metabolites exhibiting a wide variety of biological activity, such as antibiotics, antitumor and anti-infection agents, plant growth promoters and enzymes, and may contribute to their host plants by promoting growth and enhancing their ability of withstanding the environmental stresses. These microorganisms may represent an underexplored reservoir of novel species of potential interest in the discovery of novel lead compounds and for exploitation in pharmaceutical, agriculture and industry. This review focuses on new findings in the isolation methods, bio- and chemical diversity of endophytic actinobacteria and reveals the potential biotechnological application. The facing problems and strategies for biodiversity research and bioactive natural products producing are also discussed.

334 citations


Cites background from "Studies on a strain of Kitasatospor..."

  • ...isolated from Taxus baccata in Italy (Caruso et al. 2000; Janso and Carter 2010)....

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  • ...Considering that endophytic actinobacteria live in close association with their host plants and the long co-evolution relationship, there is a real possibility that genes involved in natural products biosynthesis could be exchanged via horizontal gene transfer (HGT) between microbes and plants, resulting in production of plant-derived compounds by a microbe such as the paclitaxel-producing Kitasatospora sp. isolated from Taxus baccata in Italy (Caruso et al. 2000; Janso and Carter 2010)....

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  • ...…biosynthesis could be exchanged via horizontal gene transfer (HGT) between microbes and plants, resulting in production of plant-derived compounds by a microbe such as the paclitaxel-producing Kitasatospora sp. isolated from Taxus baccata in Italy (Caruso et al. 2000; Janso and Carter 2010)....

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Journal ArticleDOI

246 citations

Journal ArticleDOI
TL;DR: How advanced chemical, biotechnological and computational molecular biology methods can be used for robust exploitation of bioactive compounds from these microorganisms is focused on.

163 citations

Journal ArticleDOI
TL;DR: An attempt has been made to assign chemical class to the compounds obtained from endophytic actinobacteria, which may find applications in medicine, agriculture, and environment.
Abstract: Actinobacteria are wide spread in nature and represent the largest taxonomic group within the domain Bacteria. They are abundant in soil and have been extensively explored for their therapeutic applications. This versatile group of bacteria has adapted to diverse ecological habitats, which has drawn considerable attention of the scientific community in recent times as it has opened up new possibilities for novel metabolites that may help in solving some of the most challenging problems of the day, for example, novel drugs for drug-resistant human pathogens, affordable means to maintain ecological balance in various habitats, and alternative practices for sustainable agriculture. Traditionally, free dwelling soil actinobacteria have been the subject of intensive research. Of late, symbiotic actinobacteria residing as endophytes within the plant tissues have generated immense interest as potential source of novel compounds, which may find applications in medicine, agriculture, and environment. In the light of these possibilities, this review focuses on the diversity of endophytic actinobacteria isolated from the plants of extreme habitats and specific ecological niches. Furthermore, an attempt has been made to assign chemical class to the compounds obtained from endophytic actinobacteria. Potential therapeutic applications of these compounds and the utility of endophytic actinobacteria in agriculture and environment are discussed.

128 citations

Journal ArticleDOI
Jeffrey E. Janso1, Guy T. Carter1
TL;DR: The results suggest that tropical plants from New Guinea and the adjacent archipelago are hosts to unique endophytic actinomycetes that possess significant biosynthetic potential.
Abstract: The culturable diversity of endophytic actinomycetes associated with tropical, native plants is essentially unexplored. In this study, 123 endophytic actinomycetes were isolated from tropical plants collected from several locations in Papua New Guinea and Mborokua Island, Solomon Islands. Isolates were found to be prevalent in roots but uncommon in leaves. Initially, isolates were dereplicated to the strain level by ribotyping. Subsequent characterization of 105 unique strains by 16S rRNA gene sequence analysis revealed that 17 different genera were represented, and rare genera, such as Sphaerisporangium and Planotetraspora, which have never been previously reported to be endophytic, were quite prevalent. Phylogenetic analyses grouped many of the strains into clades distinct from known genera within Thermomonosporaceae and Micromonosporaceae, indicating that they may be unique genera. Bioactivity testing and liquid chromatography-mass spectrometry (LC-MS) profiling of crude fermentation extracts were performed on 91 strains. About 60% of the extracts exhibited bioactivity or displayed LC-MS profiles with spectra indicative of secondary metabolites. The biosynthetic potential of 29 nonproductive strains was further investigated by the detection of putative polyketide synthase (PKS) and nonribosomal peptide synthetase (NRPS) genes. Despite their lack of detectable secondary metabolite production in fermentation, most were positive for type I (66%) and type II (79%) PKS genes, and all were positive for NRPS genes. These results suggest that tropical plants from New Guinea and the adjacent archipelago are hosts to unique endophytic actinomycetes that possess significant biosynthetic potential.

115 citations

References
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Journal ArticleDOI
TL;DR: The sensitivity of the commonly used progressive multiple sequence alignment method has been greatly improved and modifications are incorporated into a new program, CLUSTAL W, which is freely available.
Abstract: The sensitivity of the commonly used progressive multiple sequence alignment method has been greatly improved for the alignment of divergent protein sequences. Firstly, individual weights are assigned to each sequence in a partial alignment in order to down-weight near-duplicate sequences and up-weight the most divergent ones. Secondly, amino acid substitution matrices are varied at different alignment stages according to the divergence of the sequences to be aligned. Thirdly, residue-specific gap penalties and locally reduced gap penalties in hydrophilic regions encourage new gaps in potential loop regions rather than regular secondary structure. Fourthly, positions in early alignments where gaps have been opened receive locally reduced gap penalties to encourage the opening up of new gaps at these positions. These modifications are incorporated into a new program, CLUSTAL W which is freely available.

63,427 citations

Journal ArticleDOI
TL;DR: A new method for determining nucleotide sequences in DNA is described, which makes use of the 2',3'-dideoxy and arabinon nucleoside analogues of the normal deoxynucleoside triphosphates, which act as specific chain-terminating inhibitors of DNA polymerase.
Abstract: A new method for determining nucleotide sequences in DNA is described. It is similar to the “plus and minus” method [Sanger, F. & Coulson, A. R. (1975) J. Mol. Biol. 94, 441-448] but makes use of the 2′,3′-dideoxy and arabinonucleoside analogues of the normal deoxynucleoside triphosphates, which act as specific chain-terminating inhibitors of DNA polymerase. The technique has been applied to the DNA of bacteriophage ϕX174 and is more rapid and more accurate than either the plus or the minus method.

62,728 citations


"Studies on a strain of Kitasatospor..." refers methods in this paper

  • ...The 16S rDNA was subjected directly to cycle sequencing according to the protocol described by Sanger et al. (1977)....

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Journal ArticleDOI
TL;DR: Three computer programs for comparisons of protein and DNA sequences can be used to search sequence data bases, evaluate similarity scores, and identify periodic structures based on local sequence similarity.
Abstract: We have developed three computer programs for comparisons of protein and DNA sequences. They can be used to search sequence data bases, evaluate similarity scores, and identify periodic structures based on local sequence similarity. The FASTA program is a more sensitive derivative of the FASTP program, which can be used to search protein or DNA sequence data bases and can compare a protein sequence to a DNA sequence data base by translating the DNA data base as it is searched. FASTA includes an additional step in the calculation of the initial pairwise similarity score that allows multiple regions of similarity to be joined to increase the score of related sequences. The RDF2 program can be used to evaluate the significance of similarity scores using a shuffling method that preserves local sequence composition. The LFASTA program can display all the regions of local similarity between two sequences with scores greater than a threshold, using the same scoring parameters and a similar alignment algorithm; these local similarities can be displayed as a "graphic matrix" plot or as individual alignments. In addition, these programs have been generalized to allow comparison of DNA or protein sequences based on a variety of alternative scoring matrices.

12,432 citations


"Studies on a strain of Kitasatospor..." refers methods in this paper

  • ...To find the nearest relative of strain P&U 22869, its sequence was compared with sequences of microorganisms in the EMBL and GenBank databases using the program FASTA (Pearson and Lipman, 1988)....

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Book
01 Jan 1989
TL;DR: To develop a program to print the barcodes using two commonly uses command sets and hence evaluates their ease of use for such applications, students should be able to program dot matrix printers, by manipulating bit level information and ink jet printers using page description language, such as PCL.
Abstract: 1. OBJECTIVE To develop a program to print the barcodes using two commonly uses command sets and hence evaluates their ease of use for such applications. Upon completion of this experiment, students should be able to program dot matrix printers, by manipulating bit level information and ink jet printers using page description language, such as PCL which uses raster image for graphics output. Students will also become familiar with the encoding and dimensional requirements of barcode symbologies, and the suitability of the selected printers for barcode printing. The Computer Engineering Laboratory is set up with IBM-compatible PC's installed with standard C compiler. The laboratory also has several kinds of printers for this experiment. They are classified into two groups. One group consists of dot-matrix printers and the other group consists of HP ink jet printers. In this experiment, each student will have to program a dot-matrix printer using Epson 9-pin graphics command codes in group A printers and HP PCL graphics commands for the ink jet printer in group B. The assignment of different printers is as follows: 4. INTRODUCTION Barcode labelling is widely implemented in the retail marketplace and is gaining increasing visibility in a broad range of non-retail applications. To read the information contained in a barcode symbol, a scanning device such as a wand can be used. As the scanning device is moved across the symbol, the width pattern of the bars and the spaces is analysed by the reading equipment and the original data is recovered. A number of barcodes has been developed over the years, these include UPS, interleaved 2 of 5, rationalised codabar, code 39, code 128, code 93 and code 49. The American format for article numbering is the Universal Product Code (UPC). The UPC has been successfully employed in the supermarket industry since 1973. It is designed to uniquely identify a product and its manufacturer. Refer to Appendix A for UPC specifications which are necessary for this experiment. Barcode symbols can be printed with various printing technologies and on a variety of substrate labels, tags and papers. In this experiment, plain paper will be used. Hence, the quality of printed barcode will only depend on the printing mechanism. In this experiment, students will learn to program dot matrix printers by manipulating bit level information. A brief summary of the commonly used commands is attached in Appendix B and abstract from the manuals …

8,170 citations

Journal ArticleDOI
TL;DR: Amorphous metal alloys are employed in acoustic devices dependent upon the properties of low acoustic velocity and low attenuation, such as wire, strip and bulk delay lines.
Abstract: Because a natural entity “species” cannot be recognized as a group of strains that is genetically well separated from its phylogenetic neighbors, a pragmatic approach was taken to define a species by a polyphasic approach (L. G. Wayne, D. J. Brenner, R. R. Colwell, P. A. D. Grimont, O. Kandler, M. I. Krichevsky, L. H. Moore, W. E. C. Moore, R. G. E. Murray, E. Stackebrandt, M. P. Starr, and H. G. Truper, Int. J. Syst. Bacteriol. 37:463-464, 1987), in which a DNA reassociation value of about 70% plays a dominant role. With the establishment of rapid sequence analysis of 16S rRNA and the recognition of its potential to determine the phylogenetic position of any prokaryotic organism, the role of 16S rRNA similarities in the present species definition in bacteriology needs to be clarified. Comparative studies clearly reveal the limitations of the sequence analysis of this conserved gene and gene product in the determination of relationships at the strain level for which DNA-DNA reassociation experiments still constitute the superior method. Since today the primary structure of 16S rRNA is easier to determine than hybridization between DNA strands, the strength of the sequence analysis is to recognize the level at which DNA pairing studies need to be performed, which certainly applies to similarities of 97% and higher.

6,188 citations


"Studies on a strain of Kitasatospor..." refers background in this paper

  • ...In seven cases the identity level was greater than 97% consequently requiring the DNA-DNA homology tests to identify the strain P&U 22869 at the specie level (Stackebrandt and Goebel, 1994)....

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