Species Of Amycolatopsis Research Articles

Amycolatopsis nigrescens sp. nov., an actinomycete isolated from a Roman catacomb

The taxonomic status of two actinomycetes isolated from the wall of a hypogean Roman catacomb was established based on a polyphasic investigation. The organisms were found to have chemical and morphological markers typical of members of the genus Amycolatopsis. They also shared a range of chemical, molecular and phenotypic markers which served to separate them from representatives of recognized Amycolatopsis species. The new isolates formed a branch in the Amycolatopsis 16S rRNA gene sequence tree with Amycolatopsis minnesotensis NRRL B-24435(T), but this association was not supported by a particularly high bootstrap value or by the product of the maximum-parsimony tree-making algorithm. The organisms were distinguished readily from closely related Amycolatopsis species based on a combination of phenotypic properties and from all Amycolatopsis strains by their characteristic menaquinone profiles, in which tetra-hydrogenated menaquinones with 11 isoprene units predominated. The combined genotypic and phenotypic data indicate that the isolates merit recognition as representing a novel species of the genus Amycolatopsis. The name proposed for this novel species is Amycolatopsis nigrescens sp. nov., with type strain CSC17Ta-90(T) (=HKI 0330(T)=DSM 44992(T)=NRRL B-24473(T)).

Amycolatopsis minnesotensis sp. nov., isolated from a prairie soil

Two actinomycete strains, 32U-2T and 32U-4, were isolated from a prairie soil in Minnesota and subjected to characterization by means of polyphasic taxonomy. The 16S rRNA gene sequences were determined following PCR amplification and cloning. A phylogenetic analysis, based on comparative analysis of 16S rRNA gene sequences, indicated that the organisms consistently formed a well-separated, distinct sub-branch within the radiation of the genus Amycolatopsis of the family Pseudonocardiaceae. The levels of 16S rRNA sequence similarity between the isolates and the type strains of recognized Amycolatopsis species ranged from 94.1 to 97.9 %. The highest levels of sequence similarity were found between the isolates and Amycolatopsis coloradensis (97.6-97.9 %), Amycolatopsis alba and Amycolatopsis orientalis (97.3-97.6 %) and Amycolatopsis lurida (97.2-97.5 %). Chemotaxonomic characteristics supported the phylogenetic relationships between the organisms and members of the genus Amycolatopsis. However, a broad range of phenotypic and genetic data revealed that the isolates should be classified as novel species of the genus Amycolatopsis, for which the name Amycolatopsis minnesotensis sp. nov. is proposed. The type strain is 32U-2T (=KCCM 42246T = NRRL B-24435T).

Amycolatopsis plumensis sp. nov., a novel bioactive actinomycete isolated from a New-Caledonian brown hypermagnesian ultramafic soil

The taxonomic position of an actinomycete isolated from a brown hypermagnesian ultramafic soil was examined using a polyphasic approach. The organism, which was designated SBHS Strp1(T), was found to have chemical and morphological properties typical of Amycolatopsis strains. It was most closely associated with Amycolatopsis kentuckyensis, Amycolatopsis lexingtonensis, Amycolatopsis rifamycinica, Amycolatopsis pretoriensis and Amycolatopsis tolypomycina on the basis of 16S rRNA gene sequence data, and showed a unique pattern of phenotypic properties that distinguished it from the type strains of these taxa. The combined genotypic and phenotypic data show that the organism merits description as a novel species of Amycolatopsis. The name proposed for the novel species is Amycolatopsis plumensis sp. nov.; the type strain is SBHS Strp1(T) (=DSM 44776(T)=NRRL B-24324(T)).

Reclassification of Amycolatopsis mediterranei DSM 46095 as Amycolatopsis rifamycinica sp. nov.

Previous experiments have suggested that the rifamycin-producing strain DSM 46095 might not belong to Amycolatopsis mediterranei. Analysis of its 16S rRNA gene sequence and construction of a phylogenetic tree showed most similarity to Amycolatopsis kentuckyensis NRRL B-24129T, Amycolatopsis lexingtonensis NRRL B-24129T and Amycolatopsis pretoriensis NRRL B-24133T, but the strain was probably not a member of any of these species. Results from DNA-DNA hybridization experiments and comparison of DNA profiling patterns using pulsed-field gel electrophoresis also supported the assignment of strain DSM 46095 to a novel species. Analyses of phospholipids, fatty acid methyl esters and physiological characteristics also showed that the differences between different isolates of A. mediterranei and A. mediterranei DSM 46095 were as large as those between Amycolatopsis species. Strain DSM 46095 represents a novel species of the genus Amycolatopsis for which the name Amycolatopsis rifamycinica sp. nov. is proposed, with the type strain NT 19T (=DSM 46095T=ATCC 27643T).

Evolution of Enzymatic Activity in the Enolase Superfamily: Structural Studies of the Promiscuous o-Succinylbenzoate Synthase from Amycolatopsis,

Divergent evolution of enzyme function is commonly explained by a gene duplication event followed by mutational changes that allow the protein encoded by the copy to acquire a new function. An alternate hypothesis is that this process is facilitated when the progenitor enzyme acquires a second function while maintaining the original activity. This phenomenon has been suggested to occur in the o-succinylbenzoate synthase (OSBS) from a species of Amycolatopsis that catalyzes not only the physiological syn-dehydration reaction of 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate but also an accidental racemization of N-acylamino acids [Palmer, D. R., Garrett, J. B., Sharma, V., Meganathan, R., Babbitt, P. C., and Gerlt, J. A. (1999) Biochemistry 38, 4252-4258]. To understand the molecular basis of this promiscuity, three-dimensional structures of liganded complexes of this enzyme have been determined, including the product of the OSBS reaction and three N-acylamino acid substrates for the N-acylamino acid racemase (NAAAR) reaction, N-acetylmethionine, N-succinylmethionine, and N-succinylphenylglycine, to 2.2, 2.3, 2.1, and 1.9 A resolution, respectively. These structures show how the active-site cavity can accommodate both the hydrophobic substrate for the OSBS reaction and the substrates for the accidental NAAAR reaction. As expected, the N-acylamino acid is sandwiched between lysines 163 and 263, which function as the catalytic bases for the abstraction of the alpha-proton in the (R)- and (S)-racemization reactions, respectively [Taylor Ringia, E. A., Garrett, J. B, Thoden, J. B., Holden, H. M., Rayment, I., and Gerlt, J. A. (2004) Biochemistry 42, 224-229]. Importantly, the protein forms specific favorable interactions with the hydrophobic amino acid side chain, alpha-carbon, carboxylate, and the polar components of the N-acyl linkage. Accommodation of the components of the N-acyl linkage appears to be the reason that this enzyme is capable of a racemization reaction on these substrates, whereas the orthologous OSBS from Escherichia coli lacks this functionality.

Amycolatopsis palatopharyngis sp. nov., a potentially pathogenic actinomycete isolated from a human clinical source.

The taxonomic position of an actinomycete, strain 1BDZ(T), isolated from a clinical human source was determined using a polyphasic approach. Phylogenetic analysis based on almost complete 16S rDNA sequences showed that this organism consistently formed a distinct line with the Amycolatopsis methanolica subclade within the genus Amycolatopsis, and shared moderately low 16S rDNA similarity (<96.5 %) with other species. The organism was also found to have chemical and morphological properties typical of members of the genus Amycolatopsis. A range of phenotypic characteristics readily distinguished this strain from representatives of all species of Amycolatopsis with validly published names. On the basis of these data, a novel species, Amycolatopsis palatopharyngis sp. nov., is proposed to accommodate strain 1BDZ(T) (=AS 4.1729(T)=PCM 2600(T)).

Development of cloning vectors and transformation methods for Amycolatopsis.

The genus Amycolatopsis is of industrial importance, as its species are known to produce commercial antibiotics. It belongs to the family Pseudonocardiaceae and has an eventful taxonomic history. Initially strains were identified as Streptomyces, then later as Nocardia. However, based on biochemical, morphological and molecular features, the genus Amycolatopsis, containing seventeen species, was created. The development of molecular genetic techniques for this group has been slow. The scarcity of molecular genetic tools including stable plasmids, antibiotic resistance markers, transposons, reporter genes, cloning vectors, and high efficiency transformation protocols has made progress slow, but efforts in the past decade have led to the development of cloning vectors and transformation methods for these organisms. Some of the cloning vectors have broad host range (pRL series) whereas others have limited host range (pMEA300 and pMEA100). The cloning vector pMEA300 has been completely sequenced, while only the minimal replicon (pA- rep) has been sequenced from pRL plasmids. Direct transformation of mycelia and electroporation are the most widely applicable methods for transforming species of Amycolatopsis. Conjugational transfer from Escherichia coli has been reported only in the species A. japonicum, and gene disruption and replacements using homologous recombination are now possible in some strains.

Amycolatopsis eurytherma sp. nov., a thermophilic actinomycete isolated from soil.

The taxonomic positions of two thermophilic actinomycetes isolated from soil were established in a polyphasic taxonomic study. The organisms were shown to have phenotypic properties typical of members of the genus Amycolatopsis and formed a distinct phyletic line in the Amycolatopsis methanolica 16S rDNA subclade. They also had many phenotypic properties in common and formed a genomic species that was closely related to, albeit distinct from, the type strain of A. methanolica. A range of phenotypic properties distinguished the isolates from representatives of all validly described species of Amycolatopsis. Genotypic and phenotypic data show that the two strains should be classified in the genus Amycolatopsis as a novel species, Amycolatopsis eurytherma sp. nov.; the type strain is strain NT202T (= DSM 44348T = NCIMB 13795T).

Amycolatopsis rubida sp. nov., a new Amycolatopsis species from soil.

The taxonomic position of a soil isolate, strain 13.4T, was established using a polyphasic approach. The organism was found to have chemical and morphological properties consistent with its classification in the genus Amycolatopsis. Phylogenetic analysis of the strain based on its 16S rDNA sequence showed that it forms a distinct phyletic line within members of the genus Amycolatopsis. The organism was also readily distinguished from the type strains of all validly described Amycolatopsis species by its phenotypic features. The name Amycolatopsis rubida sp. nov. is proposed for this new species. The type strain is strain 13.4T (= AS 4.1541T = JCM 10871T).

Amycolatopsis sacchari sp. nov., a moderately thermophilic actinomycete isolated from vegetable matter.

The taxonomic position of a group of moderately thermophilic actinomycetes isolated from vegetable matter was determined using a suite of genotypic and phenotypic properties. The organisms were found to share a range of chemical and morphological markers typical of members of the genus Amycolatopsis. A representative of the group, strain K24T, formed a distinct phyletic line within the range of variation occupied by the genus Amycolatopsis in the 16S rDNA tree. The strains have many phenotypic properties in common and some of these distinguish the group from representatives of the validly described species of Amycolatopsis. It is clear from the combined datasets that the strains merit recognition as a new species of Amycolatopsis. The name proposed for the new species is Amycolatopsis sacchari; the type strain is K24T (= DSM 44468T = KCTC 9863T).

Improved Detection of Amycolata and Amycolatopsis Species from Soil.

To develop new and improved compounds for future use against drug-resistant bacteria or for chemical modification, it is necessary to continue to screen for new metabolites and evaluate the potential of less known and new bacterial taxa. Selective isolation of rare actinomycetes is one of the major targets of industrial microbiologists in the search for novel compounds with therapeutic activity. Amycolata and Amycolatopsis have also been target for industrial microbiologists in this search. An improved technique, involving the microwave irradiation of soil samples followed by exposure to polyvalent Nocardia/Rhodococcus phages in order to selectively detect the members of the genera Amycolata and Amycolatopsis, has been developed. This improved technique reduced the numbers of colony forming units of unwanted bacteria on isolation plates and hence increased the chances of detecting novel Amycolata and Amycolatopsis species.

Amycolatopsis thermoflava sp. nov., a novel soil actinomycete from Hainan Island, China.

A soil isolate, which had been assigned to the genus Nocardia, was shown to have properties consistent with its classification in the genus Amycolatopsis. An almost complete nucleotide sequence of the 16S rDNA of the strain was determined following cloning and sequencing of the amplified gene. The sequence was aligned with those available for members of the family Pseudonocardiaceae and related taxa and phylogenetic trees were inferred using three tree-making algorithms. The organism consistently formed a distinct monophyletic clade with the type strain of Amycolatopsis methanolica, but DNA-DNA relatedness data showed that the two strains belonged to distinct genomic species. The organism was also distinguished from the type strains of all validly described species of Amycolatopsis using a battery of phenotypic properties. The genotypic and phenotypic data show that the strain merits recognition as a new species of the genus Amycolatopsis. The name proposed for the new species is Amycolatopsis thermoflava sp. nov. The type strain is IFO 14333T.

Amycolatopsis japonicum sp. nov., an Actinomycete Producing (S,S)-N,N'-Ethylenediaminedisuccinic Acid

Summary The generic position of an aerobic, Gram-positive organism known as actinomycete MG417-CF17 was determined following isolation of the PCR amplified 16S rRNA genes and alignment of the resultant sequence with corresponding sequences from representatives of the family Pseudonocardiaceae . The assignment of the organism to the genus Amycolatopsis was strongly supported by chemotaxonomic and morphological data. The strain was distinguished from representatives of validly described Amycolatopsis species by a number of phenotypic properties. It is proposed that strain MG417-CF17 be classified in the genus Amycolatopsis as Amycolatopsis japonicum sp. nov.

Amycolatopsis coloradensis sp. nov., the Avoparcin (LL-AV290)-Producing Strain

The strain that produces the glycopeptide antibiotic avoparcin (LL-AV290) has been described previously as a strain of “Streptomyces candidus.” Morphological and chemotaxonomic properties of this strain are typical of the genus Amycolatopsis. The results of a study of the physiological properties of this organism and its levels of DNA relatedness to previously described Amycolatopsis species supported the decision to describe a new species for this strain, for which the name Amycolatopsis coloradensis is proposed. The type strain of A. coloradensis is NRRL 3218.

Amycolatopsis alba sp. nov., Isolated from Soil

A new Amycolatopsis species isolated from soil produces a new glycopeptide antibiotic related to vancomycin. Traditional taxonomic methods and contemporary fatty acid analysis techniques were used to establish the position of this species. The hyphae fragment extensively when the organism is cultured in liquid media. The organism is characterized by white aerial hyphae that bear long chains of cylindrical conidia. The reverse side is yellowish brown; a faint light brown soluble pigment is occasionally produced. The organism has a type IV cell wall (meso-diaminopimelic acid), a type A whole-cell sugar pattern, and a type PII phospholipid pattern. Mycolic acids are not present in whole-cell hydrolysates. The major menaquinone is MK-9(H4); there is also a minor amount of MK-8(H4). The name proposed for this new species is Amycolatopsis alba. The type strain is strain A83850 (= NRRL 18532).

Amycolatopsis methanolica sp. nov., a Facultatively Methylotrophic Actinomycete

The generic position of a gram-positive, facultatively methylotrophic actinomycete known as Nocardia sp. strain 239 was determined by comparing reverse transcriptase sequences of 16S rRNA. The assignment of the organism to the genus Amycolatopsis was strongly supported by chemotaxonomic and morphological data. A comparison with the type strains of validly described Amycolatopsis species showed that the organism formed the nucleus of a new species. The name proposed for this new species is Amycolatopsis methanolica. The organism has been deposited in the National Collection of Industrial Bacteria as NCIB 11946.

Pseudoamycolata halophobica gen. nov., sp. nov.

A new genus and species, Pseudoamycolata halophobica, is proposed for two closely related strains formerly assigned to Amycolata (Nocardia) autotrophica. The following characteristics are important for defining the genus Pseudoamycolata•. a type IV cell wall composition (presence of miso-diaminopimelic acid, arabinose, and galactose); lack of mycolates; phospholipid type PII (presence of phosphatidylethanolamine); menaquinone MK-8(H4) as the major menaquinone; iso- and anteiso-branched fatty acids; and a guanine-plus-cytosine content of 72 mol%. P. halophobica is readily differentiated from morphologically similar members of the genera Amycolata and Amycolatopsis by phospholipid composition and menaquinone composition, respectively. In addition, it can be distinguished from Amycolata and Amycolatopsis species by low levels of deoxyribonucleic acid-deoxyribonucleic acid homology (12 to 15 and 7 to 10%, respectively) and a number of physiological characteristics. The type strain of P. halophobica is strain VKM Ac-1069 (= DSM 43089).