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1. Kim  BJ, Kim  CJ, Chun  J, Koh  YH, Lee  SH, Hyun  JW, Cha  CY, Kook  YH,     ( 2004 )

Phylogenetic analysis of the genera Streptomyces and Kitasatospora based on partial RNA polymerase beta-subunit gene (rpoB) sequences.

International journal of systematic and evolutionary microbiology 54 (Pt 2)
PMID : 15023980  :   DOI  :   10.1099/ijs.0.02941-0    
Abstract >>
The RNA polymerase beta-subunit genes (rpoB) of 67 Streptomyces strains, representing 57 species, five Kitasatospora strains and Micromonospora echinospora KCTC 9549 were partially sequenced using a pair of rpoB PCR primers. Among the streptomycetes, 99.7-100 % similarity within the same species and 90.2-99.3 % similarity at the interspecific level were observed by analysis of the determined rpoB sequences. The topology of the phylogenetic tree based on rpoB sequences was similar to that of 16S rDNA. The five Kitasatospora strains formed a stable monophyletic clade and a sister group to the clade comprising all Streptomyces species. Although there were several discrepancies in the details, considerable agreement was found between the results of rpoB analysis and those of numerical phenetic classification. This study demonstrates that analysis of rpoB can be used as an alternative genetic method in parallel to conventional taxonomic methods, including numerical phenetic and 16S rDNA analyses, for the phylogenetic analyses of the genera Streptomyces and Kitasatospora.
KeywordMeSH Terms
2. Sawada  N, Sakaki  T, Yoneda  S, Kusudo  T, Shinkyo  R, Ohta  M, Inouye  K,     ( 2004 )

Conversion of vitamin D3 to 1alpha,25-dihydroxyvitamin D3 by Streptomyces griseolus cytochrome P450SU-1.

Biochemical and biophysical research communications 320 (1)
PMID : 15207715  :   DOI  :   10.1016/j.bbrc.2004.05.140    
Abstract >>
Streptomyces griseolus cytochrome P450SU-1 (CYP105A1) was expressed in Escherichia coli at a level of 1.0 micromol/L culture and purified with a specific content of 18.0 nmol/mg protein. Enzymatic studies revealed that CYP105A1 had 25-hydroxylation activity towards vitamin D2 and vitamin D3. Surprisingly, CYP105A1 also showed 1alpha-hydroxylation activity towards 25(OH)D3. As mammalian mitochondrial CYP27A1 catalyzes a similar two-step hydroxylation towards vitamin D3, the enzymatic properties of CYP105A1 were compared with those of human CYP27A1. The major metabolite of vitamin D2 by CYP105A1 was 25(OH)D2, while the major metabolites by CYP27A1 were both 24(OH)D2 and 27(OH)D2. These results suggest that CYP105A1 recognizes both vitamin D2 and vitamin D3 in a similar manner, while CYP27A1 does not. The Km values of CYP105A1 for vitamin D2 25-hydroxylation, vitamin D3 25-hydroxylation, and 25-hydroxyvitamin D3 1alpha-hydroxylation were 0.59, 0.54, and 0.91 microM, respectively, suggesting a high affinity of CYP105A1 for these substrates.
KeywordMeSH Terms
3. Hayashi  K, Sugimoto  H, Shinkyo  R, Yamada  M, Ikeda  S, Ikushiro  S, Kamakura  M, Shiro  Y, Sakaki  T,     ( 2008 )

Structure-based design of a highly active vitamin D hydroxylase from Streptomyces griseolus CYP105A1.

Biochemistry 47 (46)
PMID : 18937506  :   DOI  :   10.1021/bi801222d    
Abstract >>
CYP105A1 from Streptomyces griseolus has the capability of converting vitamin D 3 (VD 3) to its active form, 1alpha,25-dihydroxyvitamin D 3 (1alpha,25(OH) 2D 3) by a two-step hydroxylation reaction. Our previous structural study has suggested that Arg73 and Arg84 are key residues for the activities of CYP105A1. In this study, we prepared a series of single and double mutants by site-directed mutagenesis focusing on these two residues of CYP105A1 to obtain the hyperactive vitamin D 3 hydroxylase. R84F mutation altered the substrate specificity that gives preference to the 1alpha-hydroxylation of 25-hydroxyvitamin D 3 over the 25-hydroxylation of 1alpha-hydroxyvitamin D 3, opposite to the wild type and other mutants. The double mutant R73V/R84A exhibited 435- and 110-fold higher k cat/ K m values for the 25-hydroxylation of 1alpha-hydroxyvitamin D 3 and 1alpha-hydroxylation of 25-hydroxyvitamin D 3, respectively, compared with the wild-type enzyme. These values notably exceed those of CYP27A1, which is the physiologically essential VD 3 hydroxylase. Thus, we successfully generated useful enzymes of altered substrate preference and hyperactivity. Structural and kinetic analyses of single and double mutants suggest that the amino acid residues at positions 73 and 84 affect the location and conformation of the bound compound in the reaction site and those in the transient binding site, respectively.
KeywordMeSH Terms
4. O'Keefe  DP, Gibson  KJ, Emptage  MH, Lenstra  R, Romesser  JA, Litle  PJ, Omer  CA,     ( 1991 )

Ferredoxins from two sulfonylurea herbicide monooxygenase systems in Streptomyces griseolus.

Biochemistry 30 (2)
PMID : 1846297  :   DOI  :   10.1021/bi00216a021    
Abstract >>
We have purified and characterized two ferredoxins, designated Fd-1 and Fd-2, from the soluble protein fraction of sulfonylurea herbicide induced Streptomyces griseolus. These cells have previously been shown to contain two inducible cytochromes P-450, P-450SU1 (CYP105A1) and P-450SU2 (CYP105B1), responsible for herbicide metabolism [O'Keefe, D. P., Romesser, J. A., & Leto, K. J. (1988) Arch. Microbiol. 149, 406-412]. Although Fd-2 is more effective, either ferredoxin can restore sulfonylurea monooxygenase activity to an aerobic mixture of NADPH, spinach ferredoxin:NADP oxidoreductase, purified cytochrome P-450SU1, and herbicide substrate. The gene for Fd-1 is located in the genome just downstream of the gene for cytochrome P-450SU1; the gene for Fd-2 follows the gene for P-450SU2. The deduced amino acid sequences of the two ferredoxins show that, if monomeric, each has a molecular mass of approximately 7 kDa, and alignment of the two sequences demonstrates that they are approximately 52% positionally identical. The spectroscopic properties and iron and acid-labile sulfide contents of both ferredoxins suggest that, as isolated, each contains a single [3Fe-4S] cluster. The presence of only three cysteines in Fd-1 and comparisons with three [4Fe-4S] ferredoxins with high sequence similarity suggest that both Fd-1 and Fd-2 have an alanine in the position where these [4Fe-4S] proteins have a fourth cysteine ligand to the cluster. Transformation of Streptomyces lividans, a strain unable to metabolize sulfonylureas, with DNA encoding both P-450SU1 and Fd-1 results in cells capable of herbicide metabolism. S. lividans transformants encoding only cytochrome P-450SU1 do not metabolize herbicide.(ABSTRACT TRUNCATED AT 250 WORDS)
KeywordMeSH Terms
5. Sugimoto  H, Shinkyo  R, Hayashi  K, Yoneda  S, Yamada  M, Kamakura  M, Ikushiro  S, Shiro  Y, Sakaki  T,     ( 2008 )

Crystal structure of CYP105A1 (P450SU-1) in complex with 1alpha,25-dihydroxyvitamin D3.

Biochemistry 47 (13)
PMID : 18314962  :   DOI  :   10.1021/bi7023767    
Abstract >>
Vitamin D 3 (VD 3), a prohormone in mammals, plays a crucial role in the maintenance of calcium and phosphorus concentrations in serum. Activation of VD 3 requires 25-hydroxylation in the liver and 1alpha-hydroxylation in the kidney by cytochrome P450 (CYP) enzymes. Bacterial CYP105A1 converts VD 3 into 1alpha,25-dihydroxyvitamin D 3 (1alpha,25(OH) 2D 3) in two independent reactions, despite its low sequence identity with mammalian enzymes (<21% identity). The present study determined the crystal structures of a highly active mutant (R84A) of CYP105A1 from Streptomyces griseolus in complex and not in complex with 1alpha,25(OH) 2D 3. The compound 1alpha,25(OH) 2D 3 is positioned 11 A from the iron atom along the I helix within the pocket. A similar binding mode is observed in the structure of the human CYP2R1-VD 3 complex, indicating a common substrate-binding mechanism for 25-hydroxylation. A comparison with the structure of wild-type CYP105A1 suggests that the loss of two hydrogen bonds in the R84A mutant increases the adaptability of the B' and F helices, creating a transient binding site. Further mutational analysis of the active site reveals that 25- and 1alpha-hydroxylations share residues that participate in these reactions. These results provide the structural basis for understanding the mechanism of the two-step hydroxylation that activates VD 3.
KeywordMeSH Terms
6. Guo  Y, Zheng  W, Rong  X, Huang  Y,     ( 2008 )

A multilocus phylogeny of the Streptomyces griseus 16S rRNA gene clade: use of multilocus sequence analysis for streptomycete systematics.

International journal of systematic and evolutionary microbiology 58 (Pt 1)
PMID : 18175701  :   DOI  :   10.1099/ijs.0.65224-0    
Abstract >>
Streptomycetes are a complex group of actinomycetes that produce diverse bioactive metabolites of commercial significance. Systematics can provide a useful framework for identifying species that may produce novel metabolites. However, previously proposed approaches to the systematics of Streptomyces have suffered from either poor interlaboratory comparability or insufficient resolution. In particular, the Streptomyces griseus 16S rRNA gene clade is the most challenging and least defined group within the genus Streptomyces in terms of phylogeny. Here we report the results of a multilocus sequence analysis scheme developed to address the phylogeny of this clade. Sequence fragments of six housekeeping genes, atpD, gyrB, recA, rpoB, trpB and 16S rRNA, were obtained for 53 reference strains that represent 45 valid species and subspecies. Analysis of each individual locus confirmed the suitability of loci and the congruence of single-gene trees for concatenation. Concatenated trees of three, four, five and all six genes were constructed, and the stability of the topology and discriminatory power of each tree were analysed. It can be concluded from the results that phylogenetic analysis based on multilocus sequences is more accurate and robust for species delineation within Streptomyces. A multilocus phylogeny of six genes proved to be optimal for elucidating the interspecies relationships within the S. griseus 16S rRNA gene clade. Our multilocus sequence analysis scheme provides a valuable tool that can be applied to other Streptomyces clades for refining the systematic framework of this genus.
KeywordMeSH Terms
Bacterial Typing Techniques
Phylogeny
Sequence Analysis, DNA
7. Pet?í?ková  K, Chro?áková  A, Zelenka  T, Chrudimský  T, Pospíšil  S, Pet?í?ek  M, Krištůfek  V,     ( 2015 )

Evolution of cyclizing 5-aminolevulinate synthases in the biosynthesis of actinomycete secondary metabolites: outcomes for genetic screening techniques.

Frontiers in microbiology 6 (N/A)
PMID : 26300877  :   DOI  :   10.3389/fmicb.2015.00814     PMC  :   PMC4525017    
Abstract >>
A combined approach, comprising PCR screening and genome mining, was used to unravel the diversity and phylogeny of genes encoding 5-aminolevulinic acid synthases (ALASs, hemA gene products) in streptomycetes-related strains. In actinomycetes, these genes were believed to be directly connected with the production of secondary metabolites carrying the C5N unit, 2-amino-3-hydroxycyclopent-2-enone, with biological activities making them attractive for future use in medicine and agriculture. Unlike "classical" primary metabolism ALAS, the C5N unit-forming cyclizing ALAS (cALAS) catalyses intramolecular cyclization of nascent 5-aminolevulinate. Specific amino acid sequence changes can be traced by comparison of "classical" ALASs against cALASs. PCR screening revealed 226 hemA gene-carrying strains from 1,500 tested, with 87% putatively encoding cALAS. Phylogenetic analysis of the hemA homologs revealed strain clustering according to putative type of metabolic product, which could be used to select producers of specific C5N compound classes. Supporting information was acquired through analysis of actinomycete genomic sequence data available in GenBank and further genetic or metabolic characterization of selected strains. Comparison of 16S rRNA taxonomic identification and BOX-PCR profiles provided evidence for numerous horizontal gene transfers of biosynthetic genes or gene clusters within actinomycete populations and even from non-actinomycete organisms. Our results underline the importance of environmental and evolutionary data in the design of efficient techniques for identification of novel producers.
KeywordMeSH Terms
5-aminolevulinate synthase
C5N unit
Streptomyces
gene evolution
genetic screening
horizontal gene transfer
secondary metabolites
5-aminolevulinate synthase
C5N unit
Streptomyces
gene evolution
genetic screening
horizontal gene transfer
secondary metabolites
5-aminolevulinate synthase
C5N unit
Streptomyces
gene evolution
genetic screening
horizontal gene transfer
secondary metabolites
5-aminolevulinate synthase
C5N unit
Streptomyces
gene evolution
genetic screening
horizontal gene transfer
secondary metabolites
5-aminolevulinate synthase
C5N unit
Streptomyces
gene evolution
genetic screening
horizontal gene transfer
secondary metabolites
5-aminolevulinate synthase
C5N unit
Streptomyces
gene evolution
genetic screening
horizontal gene transfer
secondary metabolites
5-aminolevulinate synthase
C5N unit
Streptomyces
gene evolution
genetic screening
horizontal gene transfer
secondary metabolites
5-aminolevulinate synthase
C5N unit
Streptomyces
gene evolution
genetic screening
horizontal gene transfer
secondary metabolites
5-aminolevulinate synthase
C5N unit
Streptomyces
gene evolution
genetic screening
horizontal gene transfer
secondary metabolites
5-aminolevulinate synthase
C5N unit
Streptomyces
gene evolution
genetic screening
horizontal gene transfer
secondary metabolites
5-aminolevulinate synthase
C5N unit
Streptomyces
gene evolution
genetic screening
horizontal gene transfer
secondary metabolites
5-aminolevulinate synthase
C5N unit
Streptomyces
gene evolution
genetic screening
horizontal gene transfer
secondary metabolites
5-aminolevulinate synthase
C5N unit
Streptomyces
gene evolution
genetic screening
horizontal gene transfer
secondary metabolites
5-aminolevulinate synthase
C5N unit
Streptomyces
gene evolution
genetic screening
horizontal gene transfer
secondary metabolites
5-aminolevulinate synthase
C5N unit
Streptomyces
gene evolution
genetic screening
horizontal gene transfer
secondary metabolites
5-aminolevulinate synthase
C5N unit
Streptomyces
gene evolution
genetic screening
horizontal gene transfer
secondary metabolites
5-aminolevulinate synthase
C5N unit
Streptomyces
gene evolution
genetic screening
horizontal gene transfer
secondary metabolites
5-aminolevulinate synthase
C5N unit
Streptomyces
gene evolution
genetic screening
horizontal gene transfer
secondary metabolites
5-aminolevulinate synthase
C5N unit
Streptomyces
gene evolution
genetic screening
horizontal gene transfer
secondary metabolites
5-aminolevulinate synthase
C5N unit
Streptomyces
gene evolution
genetic screening
horizontal gene transfer
secondary metabolites
5-aminolevulinate synthase
C5N unit
Streptomyces
gene evolution
genetic screening
horizontal gene transfer
secondary metabolites
5-aminolevulinate synthase
C5N unit
Streptomyces
gene evolution
genetic screening
horizontal gene transfer
secondary metabolites
5-aminolevulinate synthase
C5N unit
Streptomyces
gene evolution
genetic screening
horizontal gene transfer
secondary metabolites
5-aminolevulinate synthase
C5N unit
Streptomyces
gene evolution
genetic screening
horizontal gene transfer
secondary metabolites
5-aminolevulinate synthase
C5N unit
Streptomyces
gene evolution
genetic screening
horizontal gene transfer
secondary metabolites
5-aminolevulinate synthase
C5N unit
Streptomyces
gene evolution
genetic screening
horizontal gene transfer
secondary metabolites
5-aminolevulinate synthase
C5N unit
Streptomyces
gene evolution
genetic screening
horizontal gene transfer
secondary metabolites
5-aminolevulinate synthase
C5N unit
Streptomyces
gene evolution
genetic screening
horizontal gene transfer
secondary metabolites
5-aminolevulinate synthase
C5N unit
Streptomyces
gene evolution
genetic screening
horizontal gene transfer
secondary metabolites
5-aminolevulinate synthase
C5N unit
Streptomyces
gene evolution
genetic screening
horizontal gene transfer
secondary metabolites
5-aminolevulinate synthase
C5N unit
Streptomyces
gene evolution
genetic screening
horizontal gene transfer
secondary metabolites
5-aminolevulinate synthase
C5N unit
Streptomyces
gene evolution
genetic screening
horizontal gene transfer
secondary metabolites
5-aminolevulinate synthase
C5N unit
Streptomyces
gene evolution
genetic screening
horizontal gene transfer
secondary metabolites
5-aminolevulinate synthase
C5N unit
Streptomyces
gene evolution
genetic screening
horizontal gene transfer
secondary metabolites
5-aminolevulinate synthase
C5N unit
Streptomyces
gene evolution
genetic screening
horizontal gene transfer
secondary metabolites
5-aminolevulinate synthase
C5N unit
Streptomyces
gene evolution
genetic screening
horizontal gene transfer
secondary metabolites
8.     ( 1990 )

Genes for two herbicide-inducible cytochromes P-450 from Streptomyces griseolus.

Journal of bacteriology 172 (6)
PMID : 2345149  :   DOI  :   10.1128/jb.172.6.3335-3345.1990     PMC  :   PMC209144    
Abstract >>
Streptomyces griseolus ATCC 11796 contains two inducible, herbicide-metabolizing cytochromes P-450 previously designated P-450SU1 and P-450SU2 (P-450CVA1 and P-450CVB1, respectively, using nomenclature of Nebert et al. [D. W. Nebert, M. Adesnik, M. J. Coon, R. W. Estabrook, F. J. Gonzalez, F. P. Guengerich, I. C. Gunsalus, E. F. Johnson, B. Kemper, W. Levin, I. R. Phillips, R. Sato, and M. R. Waterman, DNA 6:1-11, 1987]). Using antibodies directed against cytochrome P-450SU1, its N-terminal amino acid sequence, and amino acid composition, we cloned the suaC gene encoding cytochrome P-450SU1. Similar information about the cytochrome P-450SU2 protein confirmed that a gene cloned by cross-hybridization to the suaC gene was the subC gene encoding cytochrome P-450SU2. The suaC and subC genes were expressed in Escherichia coli, DNA for both genes was sequenced, and the deduced amino acid sequences were compared with that of the well-characterized cytochrome P-450CAM from Pseudomonas putida. Both cytochromes P-450SU1 and P-450SU2 contain several regions of strong similarity with the amino acid sequence of P-450CAM, primarily in regions of the protein responsible for attachment and coordination of the heme prosthetic group.
KeywordMeSH Terms

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