Biomaterial Database

Actinomadura rupiterrae sp. nov., isolated from cliff soil. 2012

Soon Dong Lee

Department of Science Education, Jeju National University, Jeju 690-756, Republic of Korea.

A novel actinomycete strain, designated CS5-AC15T, was isolated from a soil sample collected from a cliff on Mara Island, Jeju, Republic of Korea, and subjected to a polyphasic taxonomic analysis. The isolate produced well-developed, yellow substrate mycelium and white aerial mycelium that differentiated into straight or flexuous chains of smooth-surfaced spores. 16S rRNA gene sequence analyses showed that the organism belonged to the family Thermomonosporaceae and formed a tight cluster with the type strain of Actinomadura oligospora (97.4 % sequence similarity). Chemotaxonomic characteristics were consistent with its assignment to the genus Actinomadura in that the isolate had meso-diaminopimelic acid as the diagnostic diamino acid in the cell wall, madurose as the characteristic sugar, N-acetyl type of murein in the peptidoglycan, MK-9(H6) and MK-9(H8) as major menaquinones and a polar lipid profile containing diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and unknown phospholipids. Mycolic acids were not detected. The predominant fatty acids were C16:0, C18:1ω9c and iso-C16:0. The DNA G+C content was 70.9 mol%. DNA relatedness of strain CS5-AC15T and A. oligospora JCM 10648T was 37.9±0.7 %. On the basis of the phenotypic, phylogenetic and DNA-DNA hybridization data, strain CS5-AC15T is assigned to a novel species of the genus Actinomadura, for which the name Actinomadura rupiterrae sp. nov. is proposed (type strain CS5-AC15T=KCTC 19559T=DSM 45251T).

UI	MeSH Term	Description	Entries
D008969	Molecular Sequence Data	Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.	Sequence Data, Molecular,Molecular Sequencing Data,Data, Molecular Sequence,Data, Molecular Sequencing,Sequencing Data, Molecular
D009693	Nucleic Acid Hybridization	Widely used technique which exploits the ability of complementary sequences in single-stranded DNAs or RNAs to pair with each other to form a double helix. Hybridization can take place between two complimentary DNA sequences, between a single-stranded DNA and a complementary RNA, or between two RNA sequences. The technique is used to detect and isolate specific sequences, measure homology, or define other characteristics of one or both strands. (Kendrew, Encyclopedia of Molecular Biology, 1994, p503)	Genomic Hybridization,Acid Hybridization, Nucleic,Acid Hybridizations, Nucleic,Genomic Hybridizations,Hybridization, Genomic,Hybridization, Nucleic Acid,Hybridizations, Genomic,Hybridizations, Nucleic Acid,Nucleic Acid Hybridizations
D010457	Peptidoglycan	A structural polymer of the bacterial cell envelope consisting of sugars and amino acids which is responsible for both shape determination and cellular integrity under osmotic stress in virtually all bacteria.	Murein,Pseudomurein
D010743	Phospholipids	Lipids containing one or more phosphate groups, particularly those derived from either glycerol (phosphoglycerides see GLYCEROPHOSPHOLIPIDS) or sphingosine (SPHINGOLIPIDS). They are polar lipids that are of great importance for the structure and function of cell membranes and are the most abundant of membrane lipids, although not stored in large amounts in the system.	Phosphatides,Phospholipid
D010802	Phylogeny	The relationships of groups of organisms as reflected by their genetic makeup.	Community Phylogenetics,Molecular Phylogenetics,Phylogenetic Analyses,Phylogenetic Analysis,Phylogenetic Clustering,Phylogenetic Comparative Analysis,Phylogenetic Comparative Methods,Phylogenetic Distance,Phylogenetic Generalized Least Squares,Phylogenetic Groups,Phylogenetic Incongruence,Phylogenetic Inference,Phylogenetic Networks,Phylogenetic Reconstruction,Phylogenetic Relatedness,Phylogenetic Relationships,Phylogenetic Signal,Phylogenetic Structure,Phylogenetic Tree,Phylogenetic Trees,Phylogenomics,Analyse, Phylogenetic,Analysis, Phylogenetic,Analysis, Phylogenetic Comparative,Clustering, Phylogenetic,Community Phylogenetic,Comparative Analysis, Phylogenetic,Comparative Method, Phylogenetic,Distance, Phylogenetic,Group, Phylogenetic,Incongruence, Phylogenetic,Inference, Phylogenetic,Method, Phylogenetic Comparative,Molecular Phylogenetic,Network, Phylogenetic,Phylogenetic Analyse,Phylogenetic Clusterings,Phylogenetic Comparative Analyses,Phylogenetic Comparative Method,Phylogenetic Distances,Phylogenetic Group,Phylogenetic Incongruences,Phylogenetic Inferences,Phylogenetic Network,Phylogenetic Reconstructions,Phylogenetic Relatednesses,Phylogenetic Relationship,Phylogenetic Signals,Phylogenetic Structures,Phylogenetic, Community,Phylogenetic, Molecular,Phylogenies,Phylogenomic,Reconstruction, Phylogenetic,Relatedness, Phylogenetic,Relationship, Phylogenetic,Signal, Phylogenetic,Structure, Phylogenetic,Tree, Phylogenetic
D003960	Diaminopimelic Acid	A diamino derivative of heptanedioic acid with amino groups at C-2 and C-6 and the general formula (COOH)CH(NH2)CH2CH2CH2CH(NH2)(COOH).	2,6-Diaminopimelic Acid,2,6 Diaminopimelic Acid,Acid, 2,6-Diaminopimelic,Acid, Diaminopimelic
D004269	DNA, Bacterial	Deoxyribonucleic acid that makes up the genetic material of bacteria.	Bacterial DNA
D005227	Fatty Acids	Organic, monobasic acids derived from hydrocarbons by the equivalent of oxidation of a methyl group to an alcohol, aldehyde, and then acid. Fatty acids are saturated and unsaturated (FATTY ACIDS, UNSATURATED). (Grant & Hackh's Chemical Dictionary, 5th ed)	Aliphatic Acid,Esterified Fatty Acid,Fatty Acid,Fatty Acids, Esterified,Fatty Acids, Saturated,Saturated Fatty Acid,Aliphatic Acids,Acid, Aliphatic,Acid, Esterified Fatty,Acid, Saturated Fatty,Esterified Fatty Acids,Fatty Acid, Esterified,Fatty Acid, Saturated,Saturated Fatty Acids
D000192	Actinomycetales	An order of gram-positive, primarily aerobic BACTERIA that tend to form branching filaments.	Corynebacteriaceae,Coryneform Group
D001482	Base Composition	The relative amounts of the PURINES and PYRIMIDINES in a nucleic acid.	Base Ratio,G+C Composition,Guanine + Cytosine Composition,G+C Content,GC Composition,GC Content,Guanine + Cytosine Content,Base Compositions,Base Ratios,Composition, Base,Composition, G+C,Composition, GC,Compositions, Base,Compositions, G+C,Compositions, GC,Content, G+C,Content, GC,Contents, G+C,Contents, GC,G+C Compositions,G+C Contents,GC Compositions,GC Contents,Ratio, Base,Ratios, Base