ABSTRACT
A novel mangrove soil-derived actinomycete, strain S2-29T, was found to be most closely related to Saccharopolyspora karakumensis 5K548T based on 16 S rRNA sequence (99.24% similarity) and genomic phylogenetic analyses. However, significant divergence in digital DNA-DNA hybridization, average nucleotide identity, and unique biosynthetic gene cluster possession distinguished S2-29T as a distinct Saccharopolyspora species. Pan genome evaluation revealed exceptional genomic flexibility in genus Saccharopolyspora, with > 95% accessory genome content. Strain S2-29T harbored 718 unique genes, largely implicated in energetic metabolisms, indicating different metabolic capacities from its close relatives. Several uncharacterized biosynthetic gene clusters in strain S2-29T highlighted the strain's untapped capacity to produce novel functional compounds with potential biotechnological applications. Designation as novel species Saccharopolyspora mangrovi sp. nov. (type strain S2-29T = JCM 34,548T = CGMCC 4.7716T) was warranted, expanding the known Saccharopolyspora diversity and ecology. The discovery of this mangrove-adapted strain advances understanding of the genus while highlighting an untapped source of chemical diversity.
Subject(s)
DNA, Bacterial , Genome, Bacterial , Phylogeny , RNA, Ribosomal, 16S , Saccharopolyspora , Soil Microbiology , Saccharopolyspora/genetics , Saccharopolyspora/metabolism , Saccharopolyspora/classification , RNA, Ribosomal, 16S/genetics , DNA, Bacterial/genetics , Multigene Family , Genomics , Sequence Analysis, DNA , Wetlands , Nucleic Acid Hybridization , Bacterial Typing TechniquesABSTRACT
A novel Gram-stain-positive, aerobic, non-motile actinobacterium, designated strain E2AT, was isolated from a coral sample and examined using a polyphasic taxonomic approach. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain E2AT formed a distinct phyletic lineage in the genus Saccharopolyspora and was closely related to S. cavernae CCTCC AA 2012022T (96.4â%) and S. lacisalsi CCTCC AA 2010012T (95.3â%). The isolate grew at 15-35 °C, pH 5-12 and in the presence of 1-16â% (w/v) NaCl. The cell-wall diamino acid was meso-DAP. Major fatty acids identified were iso-C15â:â0, iso-C16â:â0 and C17â:â1 ω8c. The predominant menaquinone was MK-9(H4). The polar lipids detected were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylmethylethanolamine, one unidentified glycolipid, one unidentified phospholipid and one unidentified aminolipid. The genomic DNA G+C content was 68.6 mol%. Based on the data from the polyphasic taxonomic study reported here, strain E2AT represents a novel species within the genus Saccharopolyspora, for which the name Saccharopolyspora coralli sp. nov. is proposed. The type strain is E2AT=(JCM 31844T=MCCC 1A17150T).
Subject(s)
Anthozoa/microbiology , Phylogeny , Saccharopolyspora/classification , Animals , Bacterial Typing Techniques , Base Composition , DNA, Bacterial/genetics , Fatty Acids/chemistry , Glycolipids/chemistry , Phospholipids/chemistry , RNA, Ribosomal, 16S/genetics , Saccharopolyspora/isolation & purification , Sequence Analysis, DNA , Vitamin K 2/analogs & derivatives , Vitamin K 2/chemistryABSTRACT
Actinomycetes are a rich source for secondary metabolites with a diverse array of biological activities. Among the various genera of actinomycetes, the genus Saccharopolyspora has long been recognized as a potential source for antibiotics and other therapeutic leads that belong to diverse classes of natural products. Members of the genus Saccharopolyspora have been widely reported from several natural sources including both terrestrial and marine environments. A plethora of this genus has been chemically investigated for the production of novel natural products with interesting pharmacological effects. Therefore, Saccharopolyspora is considered one of the pharmaceutical important genera that could provide further chemical diversity with potential lead compounds. In this review, the literature from 1976 until December 2018 was covered, providing a comprehensive survey of all natural products derived from this genus and their semi-synthetic derivatives along with their biological activities, whenever applicable. Moreover, the biological diversity of Saccharopolyspora species and their habitats were also discussed.
Subject(s)
Biological Products/metabolism , Saccharopolyspora/metabolism , Animals , Anti-Bacterial Agents/chemistry , Anti-Bacterial Agents/metabolism , Anti-Bacterial Agents/pharmacology , Biological Products/chemistry , Biological Products/pharmacology , Ecosystem , Humans , Saccharopolyspora/chemistry , Saccharopolyspora/classification , Saccharopolyspora/geneticsABSTRACT
A novel actinomycete, designated as strain H219T, was isolated from rhizosphere soil collected under an Elephant ear plant (Colocasiaesculenta) in Bangkok, Thailand. Strain H219T was characterised using a polyphasic approach. Phylogenetic analysis of the 16S rRNA gene sequences revealed that this isolate was most closely related to Saccharopolyspora tripterygii JCM 32123T (97.6â%), Saccharopolyspora dendranthemae NBRC 108675T (97.5â%) and Saccharopolyspora flava NBRC 16345T (97.5â%). However, DNA-DNA hybridization analyses showed a low relatedness in the range of 39-48â% between the novel isolate and the above closely related strains. The cell-wall peptidoglycan of strain H219T contained meso-diaminopimelic acid. The diagnostic whole-cell sugars consisted of arabinose and galactose. The cellular fatty acid profile mainly comprised iso-C16â:â0, anteiso-C17â:â0, iso-C15â:â0, and 10-methyl C17â:â0. The major menaquinone was MK-9(H4). The detected phospholipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylethanolamine-containing hydroxylated fatty acids and an unknown phospholipid. The DNA G+C content was 70.6 mol%. Strain H219T represented chemotaxonomic and morphological characteristics that were consistent with members of the genus Saccharopolyspora. However, strain H219T could be distinguished from closely related strains by several phenotypic properties. Based on the data from the polyphasic studies, we propose that strain H219T is a novel species within the genus Saccharopolyspora, Saccharopolysporarhizosphaerae sp. nov. The type strain is H219T (=TBRC 8564T=NBRC 113388T).
Subject(s)
Colocasia/microbiology , Phylogeny , Rhizosphere , Saccharopolyspora/classification , Soil Microbiology , Bacterial Typing Techniques , Base Composition , DNA, Bacterial/genetics , Diaminopimelic Acid/chemistry , Fatty Acids/chemistry , Nucleic Acid Hybridization , Peptidoglycan/chemistry , Phospholipids/chemistry , RNA, Ribosomal, 16S/genetics , Saccharopolyspora/isolation & purification , Sequence Analysis, DNA , Thailand , Vitamin K 2/analogs & derivatives , Vitamin K 2/chemistryABSTRACT
A novel halophilic, Gram-positive and aerobic actinobacterium, designated strain AFM 20147T, was isolated from a sediment sample collected from Xiaochaidan Salt Lake of Qinghai, China. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain AFM 20147T belongs to the genus Saccharopolyspora, shows high sequence similarities to Saccharopolyspora griseoalba AFM 10238T (99.41%) and Saccharopolyspora halophila YIM 90500T (98.20%), and has low similarities (below 98.0%) with other members of the genus. The DNA-DNA relatedness values of strain AFM 20147T with S. griseoalba AFM 10238T and S. halophila YIM 90500T were 40 ± 1.7% and 37 ± 2.3%, respectively. Optimal growth was found to occur at 28 °C, pH 7.5 and in the presence of 7.5% (w/v) NaCl. Strain AFM 20147T was found to contain meso-diaminopimelic acid as the cell wall diamino acid, and galactose and arabinose as the whole cell sugars. The major fatty acids were identified as iso-C15:0, iso-C16:0 and anteiso-C17:0. The major polar lipids were identified as diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylinositol and phosphatidylcholine. MK-9(H4) was found to be the predominant menaquinone and the DNA G+C content was determined to be 67.8 mol%. DNA-DNA relatedness data, together with phenotypic and chemotaxonomic differences, clearly distinguish the isolate from its close neighbours. On the basis of the data from this polyphasic analysis, a novel species Saccharopolyspora qinghaiensis sp. nov. is proposed. The type strain is S. qinghaiensis AFM 20147T (=KCTC 49190T =CGMCC 4.7556T).
Subject(s)
Lakes/microbiology , Saccharopolyspora/isolation & purification , Bacterial Typing Techniques , Base Composition , China , DNA, Bacterial/genetics , Fatty Acids/chemistry , Fatty Acids/metabolism , Lakes/analysis , Phylogeny , RNA, Ribosomal, 16S/genetics , Saccharopolyspora/classification , Saccharopolyspora/genetics , Saccharopolyspora/metabolism , Sodium Chloride/analysis , Sodium Chloride/metabolismABSTRACT
Strain SYSU D8010T was isolated from a desert sand sample collected in Saudi Arabia. The taxonomic position of the isolate was investigated by the polyphasic taxonomic approach. The isolate was found to be Gram-positive and aerobic. The strain was able to grow at 14-40 °C, pH 5.0-9.0 and in the presence of up to 22â% (w/v) NaCl. Strain SYSU D8010T contained meso-diaminopimelic acid as cell-wall diamino acid, and arabinose, fucose, galactose, glucose and rhamnose as the whole-cell sugars. The primary polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol, phosphatidylinositol and phosphatidylinositolmannosides. Menaquinone MK-9(H4) was detected as the respiratory quinone; and anteiso-C17â:â0, iso-C16â:â0, iso-C15â:â0 and iso-C17â:â0 as the predominant fatty acids. Pairwise comparison of the 16S rRNA gene sequences indicated that strain SYSU D8010T had a sequence similarity of 97.8â% to Saccharopolyspora halophila YIM 90500T. The genomic DNA G+C content of strain SYSU D8010T was determined to be 69.9 mol%. Based on the analyses of the phenotypic, genotypic and phylogenetic characteristics, strain SYSU D8010T was determined to represent a novel species of the genus Saccharopolyspora, for which the name Saccharopolyspora deserti sp. nov. is proposed. The type strain of the species is SYSU D8010T (=KCTC 39989T=CPCC 204620T).
Subject(s)
Desert Climate , Phylogeny , Saccharopolyspora/classification , Salinity , Bacterial Typing Techniques , Base Composition , DNA, Bacterial/genetics , Diaminopimelic Acid/chemistry , Fatty Acids/chemistry , Phospholipids/chemistry , RNA, Ribosomal, 16S/genetics , Saccharopolyspora/genetics , Saccharopolyspora/isolation & purification , Saudi Arabia , Sequence Analysis, DNA , Vitamin K 2/analogs & derivatives , Vitamin K 2/chemistryABSTRACT
A novel Saccharopolyspora strain, designated 3SS5-12T, isolated from mangrove sediment collected from Ranong Province is described. The strain was characterized by pale yellow branching aerial mycelium which differentiated into flexuous chains of spores covered with tufts of short curved hairs. The whole-cell hydrolysates of the strain contained meso-diaminopimelic acid as the diagnostic diamino acid, with arabinose, galactose and ribose as the main sugars. A major menaquinone of this strain was MK-9(H4). Mycolic acids were absent. The DNA G+C content of the genomic DNA was 69.4 mol%. The predominant cellular fatty acids were iso-C16â:â0 and anteiso-C17â:â0. Polar lipids consisted of diphosphatidylglycerol, hydroxy-phosphatidylethanolamine, hydroxy-phosphatidylmonomethylethanolamine, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylcholine, phosphatidylglycerol, phosphatidylinositol, unidentified phospholipids and unidentified lipids. Phylogenetic determination based on 16S rRNA gene sequences indicated that the organism was classified in the genus Saccharopolyspora and highly similar to Saccharopolyspora jiangxiensis W12T (98.8â% sequence similarity), Saccharopolyspora hirsutasubsp. kobensis JCM 9109T (98.8â%), Saccharopolyspora antimicrobica I05-00074T (98.2â%) and Saccharopolyspora indica VRC122T (98.1â%). Evidence from the chemotaxonomic, phenotypic and molecular systematic data indicated that strain 3SS5-12T should be classified as a representing novel species of the genus Saccharopolyspora, for which the name Saccharopolyspora maritima sp. nov. is proposed. The type strain is 3SS5-12T (=TBRC 7048T=NBRC 112863T).
Subject(s)
Avicennia/microbiology , Geologic Sediments/microbiology , Phylogeny , Saccharopolyspora/classification , Bacterial Typing Techniques , Base Composition , DNA, Bacterial/genetics , Diaminopimelic Acid/chemistry , Fatty Acids/chemistry , Humans , Phospholipids/chemistry , Pigmentation , RNA, Ribosomal, 16S/genetics , Saccharopolyspora/genetics , Saccharopolyspora/isolation & purification , Sequence Analysis, DNA , Thailand , Vitamin K 2/analogs & derivatives , Vitamin K 2/chemistryABSTRACT
A novel marine actinomycete, designated strain CMAA 1452T, was isolated from the sponge Scopalina ruetzleri collected from Saint Peter and Saint Paul Archipelago, in Brazil, and subjected to a polyphasic taxonomic investigation. The organism formed a distinct phyletic line in the Saccharopolyspora 16S rRNA gene tree and had chemotaxonomic and morphological properties consistent with its classification in this genus. It was found to be closely related to Saccharopolyspora dendranthemae KLBMP 1305T (99.5% 16S rRNA gene sequence similarity) and shared similarities of 99.3, 99.2 and 99.0â% with 'Saccharopolyspora endophytica' YIM 61095, Saccharopolyspora tripterygii YIM 65359T and 'Saccharopolyspora pathumthaniensis' S582, respectively. DNA-DNA relatedness values between the isolate and its closest phylogenetic neighbours, namely S. dendranthemae KLBMP 1305T, 'S. endophytica' YIM 61095 and S. tripterygii YIM 65359T, were 53.5, 25.8 and 53.2â%, respectively. Strain CMAA 1452T was also distinguished from the type strains of these species using a range of phenotypic features. On the basis of these results, it is proposed that strain CMAA 1452T (=DSM 103218T=NRRL B-65384T) merits recognition as the type strain of a novel Saccharopolyspora species, Saccharopolyspora spongiae sp. nov.
Subject(s)
Phylogeny , Porifera/microbiology , Saccharopolyspora/classification , Animals , Bacterial Typing Techniques , Base Composition , Brazil , DNA, Bacterial/genetics , Nucleic Acid Hybridization , RNA, Ribosomal, 16S/genetics , Saccharopolyspora/genetics , Saccharopolyspora/isolation & purification , Sequence Analysis, DNAABSTRACT
A novel halophilic actinomycete strain, designated TRM 46074T, was isolated from Aiding salt lake in Turpan Basin, north-west China. Strain TRM 46074T was aerobic, Gram-stain-positive and grew optimally with 12â% (w/v) NaCl. The strain was observed to produce sparse aerial mycelium with long chains of spores that were non-motile and oval or spherical in shape with a rough or smooth surface; substrate mycelium was branched and well developed. The cell wall was determined to contain meso-diaminopimelic acid; the diagnostic whole-cell sugars were galactose, arabinose and ribose. The diagnostic polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphatidylglycerol and phosphatidylinositol. The predominant menaquinones were MK-9(H4), MK-10(H8) and MK-10(H4). The G+C content of the DNA was 70.9 mol%. The major fatty acids were anteiso-C17â:â0, iso-C15â:â0, iso-C16â:â0 and iso-C17â:â0. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain TRM 46074T belongs to the genus Saccharopolyspora. Strain TRM 46074T had 16S rRNA gene sequence similarity of 99.6â% with the closest described species, Saccharopolyspora ghardaiensis H53T. DNA-DNA hybridization between strain TRM 46074T and Saccharopolysporaghardaiensis H53T showed 58.6â% relatedness. On the basis of the evidence from a polyphasic study, strain TRM 46074T is considered to represent a novel species in the genus Saccharopolyspora, for which the name Saccharopolyspora aidingensis sp. nov. is proposed. The type strain is TRM 46074T (=CCTCC AA 2012014T=JCM 30185T).
Subject(s)
Lakes/microbiology , Phylogeny , Saccharopolyspora/classification , Salinity , Bacterial Typing Techniques , Base Composition , China , DNA, Bacterial/genetics , Diaminopimelic Acid/chemistry , Fatty Acids/chemistry , Nucleic Acid Hybridization , Phospholipids/chemistry , RNA, Ribosomal, 16S/genetics , Saccharopolyspora/genetics , Saccharopolyspora/isolation & purification , Sequence Analysis, DNA , Vitamin K 2/chemistryABSTRACT
A Gram-positive, halophilic actinobacterial strain Miq-12T was isolated from Meighan wetland in Iran. Strain Miq-12T was strictly aerobic, catalase positive and oxidase negative. The isolate grew at 12-25â% NaCl, at 30-50 °C and pH 5.5-10.5. The optimum NaCl, temperature and pH for growth were 15-20â%, 40 °C and 7.0-8.0, respectively. The cell wall of strain Miq-12T contained meso-diaminopimelic acid as diagnostic diamino acid and arabinose as whole-cell sugar. The polar lipid pattern consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine and phosphatidylinositol. It synthesized cellular fatty acids of anteiso and iso-branched types, anteiso-C17â:â0, iso-C17:0, iso-C15:0, iso-C16â:â0. The major respiratory quinone was MK-9(H4). The G+C content of its genomic DNA was 72.1 mol%. Phylogenetic analysis based on 16S rRNA gene sequence comparison revealed that strain Miq-12T belongs to the family Pseudonocardiaceae, constituted a separate clade, and showed the closest phylogenetic similarity to Saccharopolyspora aidingensis TRM 46074T (96.99â%) and Saccharopolyspora ghardaiensis CCUG 63370T (96.92â%). On the basis of phylogenetic analysis, phenotypic and chemotaxonomic characteristics, a novel genus and species of the family Pseudonocardiaceae, Salinifilum proteinilyticum gen. nov., sp. nov., are proposed. The type strain is Miq-12T (=IBRCM 11033T=LMG 28390T). We also propose that S. aidingensis and S. ghardaiensis should be transferred to this new genus and be named Salinifilum aidingensis comb. nov. and Salinifilum ghardaiensis comb. nov., respectively. The type strain of Salinifilum aidingensis comb. nov. is TRM 46074T (=CCTCCAA 2012014T=JCM 30185T) and the type strain of Salinifilum ghardaiensis comb. nov. is CCUG 63370T (=DSM 45606T=CECT 8304T).
Subject(s)
Actinobacteria/classification , Phylogeny , Saccharopolyspora/classification , Wetlands , Actinobacteria/genetics , Actinobacteria/isolation & purification , Bacterial Typing Techniques , Base Composition , DNA, Bacterial/genetics , Diaminopimelic Acid/chemistry , Fatty Acids/chemistry , Halobacteriales/classification , Iran , Phospholipids/chemistry , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , Vitamin K 2/analogs & derivatives , Vitamin K 2/chemistryABSTRACT
A Saccharopolyspora strain, designated CR3506T, isolated from a soil sample collected from Sungurlu, Corum, Turkey, was examinated using a polyphasic approach. Phylogenetic analysis based on an almost-complete 16S rRNA gene sequence analysis showed that the strain is closely related to the type strains of Saccharopolyspora spinosa NRRL 18395T (99.1%), Saccharopolyspora phatthalungensis NRRL B-24798T (98.4%) and Saccharopolyspora shandongensis 88T (98.1%); low levels of DNA-DNA relatedness were found between the isolate and S. spinosa and S. phatthalungensis (<50%). Strain CR3506T was found to have chemotaxonomic and phylogenetic properties consistent with its classification in the genus Saccharopolyspora. The strain contained meso-diaminopimelic acid as the diagnostic diamino acid. Whole-cell hydrolysates contained arabinose and galactose. The polar lipids were identified as phosphatidylmethylethanolamine, phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol and phosphatidylinositol. The predominant menaquinones (>10%) were MK-9(H4) and MK-8(H4). Major fatty acids were (>10%) iso-C16:0, C15:03OH, C18:0 and iso-C15:0. Further, the morphological, physiological and biochemical characteristics of strain CR3506T are distinct from S. spinosa and other species of the genus Saccharopolyspora with which this strain has high 16S rRNA gene sequence similarity (98.0-98.5%). Strain CR3506T has antimicrobial activity against Bacillus subtilis NRRL B-209, Citrobacter freundi NRRL B-2643 and Staphylococcus aureus ATCC 29213. Consequently, it is proposed that strain CR3506T represents a novel Saccharopolyspora species for which the name Saccharopolyspora hattusasensis sp. nov. is proposed. The type strain is CR3506T (=KCTC 29104T = DSM 45715T).
Subject(s)
Saccharopolyspora/classification , Soil Microbiology , Bacterial Typing Techniques , Metabolomics/methods , Phylogeny , RNA, Ribosomal, 16S/genetics , Saccharopolyspora/chemistry , Saccharopolyspora/genetics , Saccharopolyspora/isolation & purification , Sequence Analysis, DNAABSTRACT
A novel thermophilic actinomycete, designated strain T3T, was isolated from a soil sample of a sugar cane field. The strain grew at 25-60 °C (optimum 37-50 °C), at pH 6.0-11.0 (optimum 7.0-9.0) and with 0-12.0 % (w/v) NaCl (optimum 0-7 %). The aerial mycelium was white and the vegetative mycelium was colourless to pale yellow. The substrate mycelium fragmented into rod-shaped elements after 4-5âdays at 50 °C. The aerial mycelium formed flexuous chains of 5-20 spores per chain; the oval-shaped spores had spiny surfaces and were non-motile. The organism contained meso-diaminopimelic acid as the diagnostic diamino acid in the cell-wall peptidoglycan. The whole-cell sugars consisted of arabinose, galactose and ribose. The cellular fatty acid profile consisted mainly of anteiso-C17 : 0, iso-C17 : 0 and iso-C16 : 0. The quinone system was composed predominantly of MK-9(H4). The phospholipids detected were diphosphatidylglycerol, phosphatidylcholine, phosphatidylinositol, phosphatidylethanolamine, phosphatidylmethylethanolamine and ninhydrin-positive glycophospholipids. The DNA G+C content of strain T3T was 71.3âmol%. The organism showed a combination of morphological and chemotaxonomic properties typical of members of the genus Saccharopolyspora. In the 16S rRNA gene tree of Saccharopolyspora it formed a distinct phyletic line and was related most closely to Saccharopolyspora thermophila 216T. However, the phenotypic characteristics of strain T3T were significantly different from those of S. thermophila 216T and DNA-DNA hybridization revealed a low level of relatedness (28.6-32.3 %) between them. Based on the phenotypic and phylogenetic data, strain T3T represents a novel species in the genus Saccharopolyspora, for which the name Saccharopolyspora subtropica sp. nov. is proposed. The type strain is T3T ( = DSM 46801T = CGMCC 4.7206T).
Subject(s)
Phylogeny , Saccharopolyspora/classification , Saccharum/microbiology , Soil Microbiology , Bacterial Typing Techniques , Base Composition , China , DNA, Bacterial/genetics , Diaminopimelic Acid/chemistry , Fatty Acids/chemistry , Nucleic Acid Hybridization , Peptidoglycan/chemistry , Phospholipids/chemistry , RNA, Ribosomal, 16S/genetics , Saccharopolyspora/genetics , Saccharopolyspora/isolation & purification , Sequence Analysis, DNA , Vitamin K 2/analogs & derivatives , Vitamin K 2/chemistryABSTRACT
A novel halotolerant actinomycete, designated strain AFM 10238T, was isolated from a sediment sample collected from the Dead Sea of Israel. The isolate grew at 15-45 °C, pH 6-12 and with 0-15 % (w/v) NaCl. Strain AFM 10238T contains meso-diaminopimelic acid as cell wall diamino acid, and galactose and arabinose as the whole cell sugars. The major polar lipids are phosphatidylcholine, phosphatidylglycerol, and diphosphatidylglycerol. Major fatty acids are iso-C16:0, iso-C17:0, iso-C15:0, anteiso-C17:0 and C17:1 ω8c. MK-9(H4) is the predominant menaquinone and the DNA G + C content is 72.7 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain AFM10238T belongs to the genus Saccharopolyspora. The 16S rRNA gene sequence similarity between strain AFM 10238T and its close neighbours, Saccharopolyspora halophila YIM 90500T , Saccharopolyspora spinosa DSM 44228T, Saccharopolyspora dendranthemae KLBMP 1305T and Saccharopolyspora cebuensis DSM 45019T were 98.2, 97.2, 97.1 and 97.0 %, respectively. Sequence similarities to other type strains of this genus were below 97 %. DNA-DNA relatedness data, together with phenotypic and chemotaxonomic differences, clearly distinguished the isolate from its close neighbours. On the basis of the data from this polyphasic analysis, a novel species Saccharopolyspora griseoalba sp. nov. is proposed. The type strain is AFM 10238T (= DSM 46,663 = CGMCC 4.7124).
Subject(s)
Saccharopolyspora/isolation & purification , Water Microbiology , Geologic Sediments/microbiology , Molecular Typing , Oceans and Seas , Phylogeny , RNA, Bacterial , RNA, Ribosomal, 16S , Saccharopolyspora/classification , Saccharopolyspora/genetics , Saccharopolyspora/ultrastructure , Soil MicrobiologyABSTRACT
Many ancient parchments are defaced by red or purple maculae associated with localized destruction of collagen fibres. Although the main characteristics of this damage were present in most of the manuscripts analysed by many authors, no common microbial or fungal denominator has been found so far, and little or no correspondence between the microbial or fungal species isolated from materials could be addressed. In this study, culture-independent molecular methods and scanning electron microscopy (SEM) were used to identify fungal and bacterial communities on parchments affected by the purple stains. Protocols for c extraction and nucleic-acid-based strategies were selected for assays examining the community structure of fungi and bacteria on biodeteriorated parchment. Both SEM and molecular analysis detected the presence of bacterial and fungal cells in the damaged areas. Halophilic, halotolerant proteolytic bacterial species were selected by the saline environment provided by the parchment samples. As common microbial denominators, members of the Actinobacteria, mainly Saccharopolyspora spp. and species of Aspergillus, were detected in all investigated cases. It is proposed that a relationship exists between the phenomenon of purple spots on ancient parchments and that of the 'red heat' phenomenon, known to be present in some products manufactured with marine salt.
Subject(s)
Aspergillus/isolation & purification , Saccharopolyspora/isolation & purification , Skin Pigmentation , Skin/microbiology , Aspergillus/classification , Aspergillus/genetics , Collagen , DNA, Bacterial/analysis , DNA, Fungal/analysis , Microscopy, Electron, Scanning , Saccharopolyspora/classification , Saccharopolyspora/genetics , Sodium ChlorideABSTRACT
A novel actinomycete strain, designated TRM 45123(T), was isolated from a hypersaline habitat in Xinjiang Province (40° 20' N 90° 49' E), north-west China. The isolate was characterized using a polyphasic approach. 16S rRNA gene sequence analysis indicated that strain TRM 45123(T) belonged to the genus Saccharopolyspora and was closely related to Saccharopolyspora gloriosae (96.7% similarity). The G+C content of the DNA was 69.07 mol%. The isolate contained meso-diaminopimelic acid as the diagnostic diamino acid, and arabinose and ribose as the major whole-cell sugars. The diagnostic phospholipids were phosphatidylethanolamine, phosphatidylcholine and phosphatidylglycerol. The predominant menaquinone was MK-9(H4). The major fatty acids were iso-C16â:â0, anteiso-C17:0, iso-C15:0 and anteiso-C15:0. On the basis of the evidence from this polyphasic study, a novel species, Saccharopolyspora halotolerans sp. nov., is proposed. The type strain of Saccharopolyspora halotolerans is TRM 45123(T) ( = CCTCC AA 2013006(T) = DSM 45990(T)).
Subject(s)
Lakes/microbiology , Phylogeny , Saccharopolyspora/classification , Water Microbiology , Bacterial Typing Techniques , Base Composition , China , DNA, Bacterial/genetics , Diaminopimelic Acid/chemistry , Ecosystem , Fatty Acids/chemistry , Molecular Sequence Data , Phospholipids/chemistry , RNA, Ribosomal, 16S/genetics , Saccharopolyspora/genetics , Saccharopolyspora/isolation & purification , Salinity , Sequence Analysis, DNA , Vitamin K 2/analogs & derivatives , Vitamin K 2/chemistryABSTRACT
Erythromycin, a medically important antibiotic, is produced by Saccharopolyspora erythraea. Unusually, the erythromycin biosynthetic gene cluster lacks a regulatory gene, and the regulation of its biosynthesis remains largely unknown. In this study, through gene deletion, complementation and overexpression experiments, we identified a novel TetR family transcriptional regulator SACE_3986 negatively regulating erythromycin biosynthesis in S. erythraea A226. When SACE_3986 was further inactivated in an industrial strain WB, erythromycin A yield of the mutant was increased by 54.2 % in average compared with that of its parent strain, displaying the universality of SACE_3986 as a repressor for erythromycin production in S. erythraea. qRT-PCR analysis indicated that SACE_3986 repressed the transcription of its adjacent gene SACE_3985 (which encodes a short-chain dehydrogenase/reductase), erythromycin biosynthetic gene eryAI and the resistance gene ermE. As determined by EMSA analysis, purified SACE_3986 protein specifically bound to the intergenic region between SACE_3985 and SACE_3986, whereas it did not bind to the promoter regions of eryAI and ermE. Furthermore, overexpression of SACE_3985 in A226 led to enhanced erythromycin A yield by at least 32.6 %. These findings indicate that SACE_3986 is a negative regulator of erythromycin biosynthesis, and the adjacent gene SACE_3985 is one of its target genes. The present study provides a basis to increase erythromycin production by engineering of SACE_3986 and SACE_3985 in S. erythraea.
Subject(s)
Bacterial Proteins/metabolism , Erythromycin/biosynthesis , Gene Expression Regulation, Bacterial/genetics , Repressor Proteins/metabolism , Saccharopolyspora/genetics , Saccharopolyspora/metabolism , Transcription Factors/metabolism , Anti-Bacterial Agents/biosynthesis , Bacterial Proteins/genetics , DNA, Intergenic/genetics , DNA, Intergenic/metabolism , Genes, Bacterial/genetics , Multigene Family/genetics , Repressor Proteins/deficiency , Repressor Proteins/genetics , Saccharopolyspora/classification , Saccharopolyspora/growth & development , Transcription Factors/deficiency , Transcription Factors/geneticsABSTRACT
BACKGROUND: S. erythraea is a Gram-positive filamentous bacterium used for the industrial-scale production of erythromycin A which is of high clinical importance. In this work, we sequenced the whole genome of a high-producing strain (E3) obtained by random mutagenesis and screening from the wild-type strain NRRL23338, and examined time-series expression profiles of both E3 and NRRL23338. Based on the genomic data and transcriptpmic data of these two strains, we carried out comparative analysis of high-producing strain and wild-type strain at both the genomic level and the transcriptomic level. RESULTS: We observed a large number of genetic variants including 60 insertions, 46 deletions and 584 single nucleotide variations (SNV) in E3 in comparison with NRRL23338, and the analysis of time series transcriptomic data indicated that the genes involved in erythromycin biosynthesis and feeder pathways were significantly up-regulated during the 60 hours time-course. According to our data, BldD, a previously identified ery cluster regulator, did not show any positive correlations with the expression of ery cluster, suggesting the existence of alternative regulation mechanisms of erythromycin synthesis in S. erythraea. Several potential regulators were then proposed by integration analysis of genomic and transcriptomic data. CONCLUSION: This is a demonstration of the functional comparative genomics between an industrial S. erythraea strain and the wild-type strain. These findings help to understand the global regulation mechanisms of erythromycin biosynthesis in S. erythraea, providing useful clues for genetic and metabolic engineering in the future.
Subject(s)
Erythromycin/biosynthesis , Genome, Bacterial , Saccharopolyspora/genetics , Transcriptome , Comparative Genomic Hybridization , Genomics/methods , Molecular Sequence Annotation , Saccharopolyspora/classification , Saccharopolyspora/metabolismABSTRACT
A Gram-positive, aerobic, non-motile actinobacterial strain, designated YIM C01235(T), was isolated from a soil sample collected from the Swallow Cave, Yunnan province, south-west China. The isolate grew at 10-30 °C, pH 6.0-9.0 and 0-8 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences revealed highest similarity to Saccharopolyspora gloriosae YIM 60513(T) (96.8 %), and lower 16S rRNA gene sequence similarities (95.1-96.7 %) with the other species of the genus Saccharopolyspora. The whole-cell hydrolysates contained meso-diaminopimelic acid (meso-DAP), arabinose and galactose. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylmethylethanolamine, two unknown glycolipids, two unknown phospholipids and one polar lipid. MK-9(H4) was the predominant menaquinone. The major fatty acids were iso-C15:0, iso-C16:0, anteiso-C15:0 and anteiso-C17:0. Mycolic acids were not detected. The genomic DNA G+C content was 69.1 mol%. These chemotaxonomic data, together with its morphological properties, were consistent with the assignment of strain YIM C01235(T) to the genus Saccharopolyspora. The results of physiological and biochemical tests allowed strain YIM C01235(T) to be differentiated phenotypically from all the recognized Saccharopolyspora species. On the basis of evidence from this polyphasic study, the novel species Saccharopolyspora cavernae sp. nov. is proposed. The type strain is YIM C01235(T) (=DSM 45825(T) = CCTCC AA 2012022(T)).
Subject(s)
Saccharopolyspora/classification , Saccharopolyspora/isolation & purification , Aerobiosis , Amino Acids/analysis , Bacterial Typing Techniques , Base Composition , Carbohydrates/analysis , Carbon/metabolism , China , Cluster Analysis , DNA, Bacterial/chemistry , DNA, Bacterial/genetics , DNA, Ribosomal/chemistry , DNA, Ribosomal/genetics , Fatty Acids/analysis , Hydrogen-Ion Concentration , Molecular Sequence Data , Nitrogen/metabolism , Phospholipids/analysis , Phylogeny , Quinones/analysis , RNA, Ribosomal, 16S/genetics , Saccharopolyspora/genetics , Sequence Analysis, DNA , Sodium Chloride/metabolism , Soil Microbiology , TemperatureABSTRACT
A halotolerant actinomycete strain, designated strain KLBMP 1305(T), was isolated from a salt marsh plant Dendranthema indicum (Linn.) Des Moul collected from the coastal region of Nantong, Jiangsu Province, in east China and was studied in detail for its taxonomic position. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that strain KLBMP 1305(T) is a member of the genus Saccharopolyspora. The 16S rRNA gene sequence similarity indicated that strain KLBMP 1305(T) was most closely related to 'Saccharopolyspora pathumthaniensis' S582(T) (99.31 %), 'Saccharopolyspora endophytica' YIM 61095(T) (99.17 %) and Saccharopolyspora tripterygii YIM 65359(T) (99.15 %); similarity to other type strains of the genus Saccharopolyspora was <97.2 %. The organism had chemical and morphological features consistent with its classification in the genus Saccharopolyspora such as meso-diaminopimelic acid as the diagnostic diamino acid in the cell wall peptidoglycan and arabinose and galactose as the diagnostic sugars. The predominant menaquinone was MK-9(H4). The polar lipids detected were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, an unknown glycolipid and an unknown lipid. The major fatty acids were iso-C16:0, iso-C15:0, anteiso-C15:0, anteiso-C17:0 and sum in feature 8 (18:1ω7c/18:1ω6c). The G+C content of the genomic DNA of the type strain was 68.7 mol%. DNA-DNA relatedness data, together with phenotypic differences, clearly distinguished the isolate from its closest relatives. On the basis of these phenotypic and genotypic data, the isolate represents a novel species, for which the name Saccharopolyspora dendranthemae sp. nov. is proposed. The type strain is KLBMP 1305(T) (=KCTC 19889(T) = NBRC 108675(T)).
Subject(s)
Chrysanthemum/microbiology , Endophytes/isolation & purification , Endophytes/physiology , Saccharopolyspora/isolation & purification , Saccharopolyspora/physiology , Salt Tolerance , Wetlands , Bacterial Typing Techniques , Base Composition , Base Sequence , China , DNA, Bacterial/genetics , Diaminopimelic Acid/metabolism , Endophytes/classification , Endophytes/genetics , Energy Metabolism , Fatty Acids , Molecular Sequence Data , Phylogeny , RNA, Ribosomal, 16S/genetics , Saccharopolyspora/classification , Saccharopolyspora/genetics , Sequence Analysis, DNA , Sodium Chloride , Vitamin K 2/analysisABSTRACT
A novel actinomycete strain, designated TRM 40133(T), was isolated from a hypersaline habitat of Tarim basin in Xinjiang Province, north-west China. Its taxonomic status was determined using a polyphasic approach. Phylogenetic analysis based on an almost-complete 16S rRNA gene sequence of the strain showed that it formed a well-seperated sub-branch within the radiation of the genus Saccharopolyspora. The highest levels of 16S rRNA gene sequence similarity was found between the strain TRM 40133(T) and Saccharopolyspora qijiaojingensis YIM 91168(T) (96.5%). The chemotaxonomic characteristics of the isolate are typical for the genus Saccharopolyspora. It contained meso-DAP as the diagnostic diamino acid. Whole cell hydrolysate contained arabinose, xylose, ribose and glucose. The diagnostic phospholipids were phosphatidylcholine, phosphatidylglycerol, phosphatidylinositol and two unknown phospholipids. The main menaquinone was MK-9(H(6)) and MK-9(H(4)). No mycolic acid was detected. The predominant cellular fatty acids were iso-C(16:0) and anteiso-C(17:0). The G+C content of the genomic DNA was 68.2 mol%. In addition, the strain TRM 40133(T) had a phenotypic profile that readily distinguished it from the recognized representatives of the genus Saccharopolyspora. The strain TRM 40133(T) therefore represents a novel species of the genus Saccharopolyspora, for which the name Saccharopolyspora lacisalsi sp. nov. is proposed. The type strain is TRM 40133(T) (=KCTC 19987(T) =CCTCC AA 2010012(T)).