Methods of cell lysis and effect of detergents for the recovery of nitrile metabolizing enzyme from Amycolatopsis sp. IITR215

Nitrile metabolizing enzymes are of great industrial interest for the selective bio-transformation of nitriles and surface modification of synthetic polymers under mild reaction conditions. In the present work, isolated strain Amycolatopsis sp. IITR215 was cultivated in the bench top bioreactor for the recovery of maximum biomass of whole cell catalyst. Effect of different lyoprotectants was studied on nitrile metabolizing enzyme from Amycolatopsis sp. IITR215 in which sorbitol proved to be an efficient lyoprotectant. In physical and mechanical methods, only 30% activity was recovered while 85% activity was achieved in the enzymatic method using 2 g/l lysozyme. Very less activity was recovered during stationary phase when cells were grown in mineral base media containing 1 g/l yeast. Therefore, recovery of intracellular enzymes was enhanced by using different concentrations of sodium cholate and deoxycholate.     

Evaluation of the antibiotic biosynthetic potential of the genus Amycolatopsis and description of Amycolatopsis circi sp. nov., Amycolatopsis equina sp. nov. and Amycolatopsis hippodromi sp. nov

Aims: To describe three new Amycolatopsis strains and assess the antibiotic biosynthetic potential of the genus. Methods and Results: Three strains, designated S1·3^T, S3·6^T and SE(8)3^T, belonging to the genus Amycolatopsis were isolated and found to cluster together by 16S rRNA and gyrB gene‐based phylogenetic analysis. Genetic distance values, based on the gyrB gene, were calculated between the strains and their closest relatives and were all above the threshold value of 0·02 that has been proposed to distinguish Amycolatopsis type strains. DNA–DNA hybridization experiments against related type strains confirmed that strain S3·6^T represents a unique genomic species. Strain S3·6^T was also found to be distinct from strains S1·3^T and SE(8)3^T, the latter two of which were also shown to be distinct from each other. Antibiotic biosynthetic genes were identified from multiple Amycolatopsis strains, and their presence was found to be phylogenetically associated. Conclusions: The data presented in this study indicate that strains S1·3^T, SE(8)3^T and S3·6^T belong to three novel species, for which the names Amycolatopsis circi sp. nov. (= DSM 45561^T = NRRL B‐24841^T), Amycolatopsis equina sp. nov. (= DSM 45563^T = NRRL B‐24842^T) and Amycolatopsis hippodromi sp. nov. (= DSM 45562^T = NRRL B‐24843^T) are proposed. Significance and Impact of the Study: Three new species of Amycolatopsis are described, and the knowledge of the antibiotic biosynthetic potential of the genus has been extended.     

Amycolatopsis bartoniae sp. nov. and Amycolatopsis bullii sp. nov., mesophilic actinomycetes isolated from arid Australian soils

The status of two mesophilic filamentous actinomycetes isolated from an arid Australian soil sample was determined using a polyphasic taxonomic approach. The isolates had chemical and morphological properties consistent with their classification in the genus Amycolatopsis, assignments that were supported by analysis of 16S rRNA gene sequence data. Isolate SF26^T formed a distinct phyletic line and hence was sharply separated from its nearest phylogenetic neighbour, Amycolatopsis sacchari DSM 44468^T. In contrast, isolate SF27^T formed a subclade in the Amycolatopsis tree with Amycolatopsis vancoresmycina DSM 44592^T but was separated readily from the latter by DNA:DNA pairing data. The two isolates were distinguished from one another and from their respective nearest phylogenetic neighbours using a range of phenotypic properties. These data indicate that the two isolates should be recognized as new species in the genus Amycolatopsis. The names proposed for these new taxa are Amycolatopsis bartoniae sp. nov. and Amycolatopsis bullii sp. nov. with isolates SF26^T (=NCIMB 14706^T = NRRL B-2846^T) and SF27^T (=NCIMB 14707^T = NRRL B-24847^T) as the respective type strains.     

PCR screening reveals unexpected antibiotic biosynthetic potential in Amycolatopsis sp. strain UM16

AIMS: To assess the antibiotic biosynthetic potential of Amycolatopsis sp. strain UM16 and eight other Amycolatopsis species. METHODS AND RESULTS: Amycolatopsis genomic DNA was screened by PCR for the glycopeptide, Type-II (aromatic) polyketide and ansamycin biosynthetic gene clusters. Amycolatopsis sp. strain UM16, which exhibits weak antitubercular activity, was shown to have the glycopeptide oxyB gene and the Type-II (aromatic) polyketide-synthase KSalpha-KSbeta tandem gene pair, but not the AHBA synthase gene. The ristocetin (glycopeptide) producer, Amycolatopsis lurida NRRL 2430(T), was shown to have the oxyB gene and the Type-II polyketide-synthase KSalpha-KSbeta tandem gene pair. Amycolatopsis alba NRRL 18532(T) was shown to have the glycopeptide oxyB gene and the AHBA synthase gene. Phylogenetic analyses using Amycolatopsis oxyB and KSalpha-KSbeta gene sequences were conducted. CONCLUSIONS: Amycolatopsis sp. strain UM16 appears to have the biosynthetic potential to produce glycopeptide and Type-II polyketide antibiotics, but not ansamycins. The potential to synthesize aromatic polyketides may be more widely distributed in Amycolatopsis than is currently recognized. SIGNIFICANCE AND IMPACT OF THE STUDY: PCR screening is a very useful tool for rapidly identifying the biosynthetic potential of an antibiotic-producing actinomycete isolate. Advanced knowledge of the type of antibiotic(s) produced will allow appropriate methods to be selected for antibiotic purification.     

Polylactide Degradation by an Amycolatopsis sp

By applying the plate count and clear-zone methods, it was confirmed that polylactide (PLA)-degrading microorganisms are sparsely distributed in soil environments. An Amycolatopsis isolate was successfully isolated. Microbial degradation of PLA film was demonstrated; i.e., about 60% of the 100-mg film initially added was degraded by the strain after 14 days of liquid culture.     

Bioconversion of lovastatin to a novel statin by Amycolatopsis sp.

3-Hydroxy-3-methylglutaryl–coenzyme A (HMG–CoA) reductase catalyzes the conversion of HMG–CoA to mevalonic acid, which plays a significant role in cholesterol synthesis. Several statins, inhibitors of HMG–CoA reductase, can be synthesized and converted by microorganisms. Among 700 strains obtained from culture collections, one strain could convert lovastatin to a novel statin, wuxistatin. The strain was identified as a member of the genus Amycolatopsis based on 16S rRNA gene sequence, morphology analysis, and chemotaxonomic properties. Wuxistatin, a novel HMG–CoA reductase inhibitor, was purified by chromatography, and the structure was determined by electrospray ionization mass and nuclear magnetic resonance spectroscopy. The results show that wuxistatin was butanoic acid, 2-methyl-,1,2,3,5,8,8a-hexahydro-5-hydroxy-7-methyl-8-[2-(tetrahydro-4-hydroxy-6-oxo-2H-pyran-2-yl) ethy]-1-naphthalenyl ester. An additional hydroxyl group was added to lovastatin at the 5-position to yield wuxistatin. This modification enhanced the intrinsic inhibitory activity (IC50) of wuxistatin (41 ± 5 nM) for fourfold compared with lovastatin (160 ± 10 nM). A stoichiometric conversion of lovastatin to wuxistatin occurred.     

细胞色素P450酶对拟无枝酸菌转化洛伐他汀的影响

无锡他汀是胆固醇合成途径中限速酶羟甲基戊二酰辅酶A(HMG—CoA)还原酶抑制剂,由洛伐他汀经拟无枝酸菌(Amycolatopsis sp.ST2710)羟基化转化产生,为研究无锡他汀转化过程,本文利用CO差光谱法在摇瓶水平考察了底物浓度、温度、pH值、溶氧等因素对具有羟基化功能的细胞色素P450酶活的变化情况,以及细胞色素P450酶变化对洛伐他汀羟基化过程中的影响。研究表明,细胞色素P450酶可能是Amycolatopsis sp.ST2710转化洛伐他汀为无锡他汀代谢途径的一个关键酶,对洛伐他汀羟基化有重要作用,这为进一步对微生物转化洛伐他汀的研究打下了基础。     

Genome sequence of Amycolatopsis sp. strain ATCC 39116, a plant biomass-degrading actinomycete

We announce the availability of a high-quality draft of the genome sequence of Amycolatopsis sp. strain 39116, one of few bacterial species that are known to consume the lignin component of plant biomass. This genome sequence will further ongoing efforts to use microorganisms for the conversion of plant biomass into fuels and high-value chemicals.     

Purification and characterization of an extracellular chitosanase produced by Amycolatopsis sp. CsO-2

Extracellular chitosanase produced by Amycolatopsis sp. CsO-2 was purified to homogeneity by precipitation with ammonium sulfate followed by cation exchange chromatography. The molecular weight of the chitosanase was estimated to be about 27,000 using SDS-polyacrylamide gel electrophoresis and gel filtration. The maximum velocity of chitosan degradation by the enzyme was attained at 55°C when the pH was maintained at 5.3. The enzyme was stable over a temperature range of 0–50°C and a pH range of 4.5–6.0. About 50% of the initial activity remained after heating at 100°C for 10 min, indicating a thermostable nature of the enzyme. The isoelectric point of the enzyme was about 8.8. The enzyme degraded chitosan with a range of deacetylation degree from 70% to 100%, but not chitin or CM-cellulose. The most susceptible substrate was 100% deacetylated chitosan. The enzyme degraded glucosamine tetramer to dimer, and pentamer to dimer and trimer, but did not hydrolyze glucosamine dimer and trimer.     

Degradation of Polycarbonate by a Polyester-Degrading Strain, Amycolatopsis sp. Strain HT-6

Amycolatopsis sp. strain HT-6, a poly(tetramethylene succinate) (PTMS)-degrading actinomycete, was observed to degrade poly(tetramethylene carbonate) (PTMC). In a liquid culture with 150 mg of PTMC film, 59% degradation was achieved, but with a low yield of cell growth. On the other hand, PTMS copolymerized with a small amount of PTMC, forming a copolyester carbonate (PEC) that was completely and rapidly degraded with a high yield of cell growth.     

Advances in the bioconversion mechanism of lovastatin to wuxistatin by Amycolatopsis sp. CGMCC 1149

Wuxistatin, a novel statin and more potent than lovastatin, was converted from lovastatin by Amycolatopsis sp. (CGMCC 1149). Product I, an intermediate product, was found in the fermentation broth, and the structure analysis showed that product I had an additional hydroxyl group at the methyl group attached to C3 compared to lovastatin, which indicates that product I is one isomer of wuxistatin. Isotope tracing experiment proved that hydroxyl group of wuxistatin was provided by product I and the reaction from product I to wuxistatin was an intramolecular transfer. Hydroxylation reaction established in a cell-free system could be inhibited by CO and enhanced by ATP, Fe²⁺, and ascorbic acid, which were consistent with the presumption that the hydroxylase was an induced cytochrome P450. Study on proteomics of Amycolatopsis sp. CGMCC 1149 suggested that three identified proteins, including integral membrane protein, Fe-S oxidoreductase, and GTP-binding protein YchF, were induced by lovastatin and required during hydroxylation reaction. In conclusion, bioconversion mechanism of wuxistatin by Amycolatopsis sp. CGMCC 1149 was proposed: lovastatin is firstly hydroxylated to product I by a hydroxylase, namely cytochrome P450, and then product I is rearranged to wuxistatin by isomerases.     

Isolation and identification of Amycolatopsis sp. strain 1119 with potential to improve cucumber fruit yield and induce plant defense responses in commercial greenhouse

Plant and Soil - The aims of this work were (i) to find a soil indicator to predict durum wheat yield response to Zn fertilization, (ii) to compare the effect of various Zn fertilization strategies...     

Amycolatopsis camponoti sp. nov., new tetracenomycin-producing actinomycete isolated from carpenter ant Camponotus vagus

An actinobacterial strain A23^T, isolated from adult ant Camponotus vagus collected in Ryazan region (Russia) and established as tetracenomycin X producer, was subjected to a polyphasic taxonomic study. Morphological characteristics of this strain included well-branched substrate mycelium and aerial hyphae fragmented into rod-shaped elements. Phylogenetic analyses based on 16S rRNA gene and genome sequences showed that strain A23^T was most closely related to Amycolatopsis pretoriensis DSM 44654^T. Average nucleotide identity and digital DNA–DNA hybridization values between the genome sequences of isolate A23^T and its closest relative, Amycolatopsis pretoriensis DSM 44654^T, were 39.5% and 88.6%, which were below the 70% and 95–96% cut-off point recommended for bacterial species demarcation, respectively. The genome size of the isolate A23^T was 10,560,374 bp with a DNA G?+?C content of 71.2%. The whole-cell hydrolysate contained meso-diaminopimelic acid and arabinose and galactose as main diagnostic sugars as well as ribose and rhamnose. It contained MK-9(H4) as the predominant menaquinone and iso-C_16:0, iso-C_15:0, anteiso-C_17:0 and C_16:0 as the major cellular fatty acids. Diphosphatidylglycerol and phosphatidylethanolamine prevailed among phospholipids. Mycolic acids were not detected. Based on the phenotypic, genomic and phylogenetic data, isolate A23^T represents a novel species of the genus Amycolatopsis, for which the name Amycolatopsis camponoti sp. nov. is proposed, and the type strain is A23^T (=?DSM 111725^T?=?VKM Ac-2882^T).

     

Construction of expression vectors for metabolic engineering of the vanillin-producing actinomycete Amycolatopsis sp. ATCC 39116

Amycolatopsis sp. ATCC 39116 is able to synthesize the important flavoring agent vanillin from cheap natural substrates. The bacterium is therefore of great interest for the industry and used for the fermentative production of vanillin. In order to improve the production of natural vanillin with Amycolatopsis sp. ATCC 39116, the strain has been genetically engineered to optimize the metabolic flux towards the desired product. Extensive metabolic engineering was hitherto hampered, due to the lack of genetic tools like functional promoters and expression vectors. In this study, we report the establishment of a plasmid-based gene expression system for Amycolatopsis sp. ATCC 39116 that allows a further manipulation of the genotype. Four new Escherichia coli–Amycolatopsis shuttle vectors harboring different promoter elements were constructed, and the functionality of these regulatory elements was proven by the expression of the reporter gene gusA, encoding a β-glucuronidase. Glucuronidase activity was detected in all plasmid-harboring strains, and remarkable differences in the expression strength of the reporter gene depending on the used promoter were observed. The new expression vectors will promote the further genetic engineering of Amycolatopsis sp. ATCC 39116 to get insight into the metabolic network and to improve the strain for a more efficient industrial use.     

Nitrile-metabolizing potential of Bacillus cereus strain FA12; Nitrilase production,purification, and characterization

Nitrile-hydrolyzing bacteria have the potential to perform useful biotransformations such as the production of industrially useful acids and amides. In this study, we report a nitrile-degrading bacterium with significant nitrile metabolism. Molecular characterization of 16S rDNA gene characterized this strain as Bacillus cereus. Medium optimization of B. cereus FA12 showed that biomass and nitrilase production was strongly supported by glucose (10 gL^{? 1}) and yeast extract (10 gL^{? 1}). Enzymatic production improved slightly in the pH range from 6.0 to 7.0. The addition of Mg⁺², Fe⁺², and Na⁺ supported biomass and nitrilase production; however, other metal ions, Co⁺² and Cu⁺², inhibited production. The apparent molecular mass of the puri?ed FA12 nitrilase as determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) was about 45 kDa. Nitrilase FA12 shows relatively high activity and stability at pH 7.0 and 40°C. Nitrilase FA12 was marginally inhibited with Ca^{+ 2} and Co⁺², whereas inhibition in the presence of dithiothreitol or DTT was 80%. The pseudo K_m (mM) values of resting cells (i.e., treating whole cells as if they were an enzyme) for acetonitrile and acetamide were determined to be 2.36 and 1.81, respectively. Under optimum situations, B. cereus FA12 resting cells produced 83 and 58 (U/mg) acetonitrile/acetamide degrading activity, respectively. Ammonia production from acetamide and acetonitrile by the B. cereus FA12 was maximum after 5 and 7 h of incubation, respectively. These results indicate that B. cereus FA12 resting cells may be used in nitrile biotransformations to produce commercially useful compounds.