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1. Zazopoulos  E, Huang  K, Staffa  A, Liu  W, Bachmann  BO, Nonaka  K, Ahlert  J, Thorson  JS, Shen  B, Farnet  CM,     ( 2003 )

A genomics-guided approach for discovering and expressing cryptic metabolic pathways.

Nature biotechnology 21 (2)
PMID : 12536216  :   DOI  :   10.1038/nbt784    
Abstract >>
Genome analysis of actinomycetes has revealed the presence of numerous cryptic gene clusters encoding putative natural products. These loci remain dormant until appropriate chemical or physical signals induce their expression. Here we demonstrate the use of a high-throughput genome scanning method to detect and analyze gene clusters involved in natural-product biosynthesis. This method was applied to uncover biosynthetic pathways encoding enediyne antitumor antibiotics in a variety of actinomycetes. Comparative analysis of five biosynthetic loci representative of the major structural classes of enediynes reveals the presence of a conserved cassette of five genes that includes a novel family of polyketide synthase (PKS). The enediyne PKS (PKSE) is proposed to be involved in the formation of the highly reactive chromophore ring structure (or "warhead") found in all enediynes. Genome scanning analysis indicates that the enediyne warhead cassette is widely dispersed among actinomycetes. We show that selective growth conditions can induce the expression of these loci, suggesting that the range of enediyne natural products may be much greater than previously thought. This technology can be used to increase the scope and diversity of natural-product discovery.
KeywordMeSH Terms
2. Arisawa  A, Matsufuji  M, Nakashima  T, Dobashi  K, Isshiki  K, Yoshioka  T, Yamada  S, Momose  H, Taguchi  S,     ( 2002 )

Streptomyces serine protease (DHP-A) as a new biocatalyst capable of forming chiral intermediates of 1,4-dihydropyridine calcium antagonists.

Applied and environmental microbiology 68 (6)
PMID : 12039725  :   DOI  :   10.1128/aem.68.6.2716-2725.2002     PMC  :   PMC123970    
Abstract >>
Streptomyces viridosporus A-914 was screened as a producer of an enzyme to effectively form chiral intermediates of 1,4-dihydropyridine calcium antagonists. The supernatant liquid of the growing culture of this strain exhibited high activity for enantioselective hydrolysis of prochiral 1,4-dihydropyridine diesters to the corresponding (4R) half esters. The responsible enzyme (termed DHP-A) was purified to apparent homogeneity and characterized. Cloning and sequence analysis of the gene for DHP-A (dhpA) revealed that the enzyme was a serine protease that is highly similar in both structural and enzymatic feature to SAM-P45, which is known as a target enzyme of Streptomyces subtilisin inhibitor (SSI), from Streptomyces albogriseolus. In a batch reaction test, DHP-A produced a higher yield of a chiral intermediate of 1,4-dihydropyridine than the commercially available protease P6. Homologous or heterologous expression of dhpA resulted in overproduction of the enzyme in culture supernatants, with 2.4- to 4.2-fold higher specific activities than in the parent S. viridosporus A-914. This indicates that DHP-A is suitable for use in reactions forming chiral intermediates of calcium antagonists and suggests the feasibility of developing DHP-A as a new commercial enzyme for use in the chiral drug industry.
KeywordMeSH Terms
3. Magnuson  TS, Ramachandran  S,     ( 2000 )

Isolation and analysis of three peroxide sensor regulatory gene homologs ahpC, ahpX and oxyR in Streptomyces viridosporus T7A--a lignocellulose degrading actinomycete.

DNA sequence : the journal of DNA sequencing and mapping 11 (1��2��)
PMID : 10902909  :  
Abstract >>
Increased lignolytic peroxidase activity has been demonstrated with the addition of sublethal doses of toxic H2O2 in Streptomyces viridosporus T7A. Until now, the effect of H2O2 at the molecular level has not been well characterized. Here, for the first time we report the isolation and analysis of three peroxide-induced gene homologs from S. viridosporus T7A; ahpC and ahpX (encoding alkyl hydroxyperoxidase subunits) and oxyR (encoding oxygen stress regulatory protein). The genome organization of these stress related genes were found to be divergently adjacent to each other. The protein sequence analysis of the oxyR homolog revealed a helix-turn-helix DNA-binding motif characteristic to the LysR of regulatory proteins induced by H2O2. The nucleotide sequence analysis of the intergenic region between ahpC and oxyR revealed that they shared a core T-n11-A, a signature protein-binding region of LysR family members. Based on similarities in sequence analysis, genetic organization, and the induction of lignin peroxidase activity upon exposure to hydrogen peroxide, we hypothesize a peroxide induction mechanism for the regulation of oxidative lignin biodegradation by S. viridosporus, possibly via use of OxyR which is also involved in regulating the peroxide stress response in this actinomycete.
KeywordMeSH Terms
DNA-Binding Proteins
Genes, Bacterial
4. Ostash  B, Saghatelian  A, Walker  S,     ( 2007 )

A streamlined metabolic pathway for the biosynthesis of moenomycin A.

Chemistry & biology 14 (1��3��)
PMID : 17379141  :   DOI  :   10.1016/j.chembiol.2007.01.008     PMC  :   PMC1936435    
Abstract >>
Moenomycin A (MmA) is a member of the phosphoglycolipid family of antibiotics, which are the only natural products known to directly target the extracellular peptidoglycan glycosyltransferases involved in bacterial cell wall biosynthesis. The structural and biological uniqueness of MmA make it an attractive starting point for the development of new antibacterial drugs. In order both to elucidate the biosynthesis of this unusual compound and to develop tools to manipulate its structure, we have identified the MmA biosynthetic genes in Streptomyces ghanaensis (ATCC14672). We show via heterologous expression of a subset of moe genes that the economy of the MmA pathway is enabled through the use of sugar-nucleotide and isoprenoid building blocks derived from primary metabolism. The work reported lays the foundation for genetic engineering of MmA biosynthesis to produce novel derivatives.
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5. Ostash  B, Makitrinskyy  R, Walker  S, Fedorenko  V,     ( 2009 )

Identification and characterization of Streptomyces ghanaensis ATCC14672 integration sites for three actinophage-based plasmids.

Plasmid 61 (3)
PMID : 19167423  :   DOI  :   10.1016/j.plasmid.2008.12.002     PMC  :   PMC2699751    
Abstract >>
Streptomyces ghanaensis produces the antibiotic moenomycin A, which is the only known direct inhibitor of bacterial peptidoglycan glycosyltransferases (transglycosylases). Recent progress in understanding moenomycin biosynthesis opens the door to the generation of novel moenomycins via biocombinatorial approaches. To realize the promise of such an approach, one needs better knowledge of the S. ghanaensis genome and diverse genetic tools for stable expression of recombinant constructs in this strain. In this respect, we report the intergeneric Escherichia coli-S. ghanaensis conjugal transfer of plasmids pRT801 and pSOK804 based on the actinophage BT1 and VWB integrase systems, respectively. The attB sites for these two plasmids and for pSET152 were characterized. In particular, sequencing revealed that a putative Arg-tRNA gene serves as an integration site for both phage VWB and pSAM2-like actinomycete integrative and conjugative element recently suggested to be widespread and functional in actinomycetes. The stability of the studied plasmids and their neutrality with respect to antibiotic production warrant their use for manipulations of S. ghanaensis genome.
KeywordMeSH Terms
6. Zhang  L, Chen  CC, Ko  TP, Huang  JW, Zheng  Y, Liu  W, Wang  I, Malwal  SR, Feng  X, Wang  K, Huang  CH, Hsu  ST, Wang  AH, Oldfield  E, Guo  RT,     ( 2016 )

Moenomycin Biosynthesis: Structure and Mechanism of Action of the Prenyltransferase MoeN5.

Angewandte Chemie (International ed. in English) 55 (15)
PMID : 26954060  :   DOI  :   10.1002/anie.201511388     PMC  :   PMC4818699    
Abstract >>
The structure of MoeN5, a unique prenyltransferase involved in the biosynthesis of the antibiotic moenomycin, is reported. MoeN5 catalyzes the reaction of geranyl diphosphate (GPP) with the cis-farnesyl group in phosphoglycolipid 5 to form the (C25) moenocinyl-sidechain-containing lipid 7. GPP binds to an allylic site (S1) and aligns well with known S1 inhibitors. Alkyl glycosides, glycolipids, can bind to both S1 and a second site, S2. Long sidechains in S2 are "bent" and co-locate with the homoallylic substrate isopentenyl diphosphate in other prenyltransferases. These observations support a MoeN5 mechanism in which 5 binds to S2 with its C6-C11 group poised to attack C1 in GPP to form the moenocinyl sidechain, with the more distal regions of 5 aligning with the distal glucose in decyl maltoside. The results are of general interest because they provide the first structures of MoeN5 and a structural basis for its mechanism of action, results that will facilitate the design of new antibiotics.
KeywordMeSH Terms
drug discovery
enzyme mechanisms
protein structure
7. Busarakam  K, Bull  AT, Girard  G, Labeda  DP, van Wezel  GP, Goodfellow  M,     ( 2014 )

Streptomyces leeuwenhoekii sp. nov., the producer of chaxalactins and chaxamycins, forms a distinct branch in Streptomyces gene trees.

Antonie van Leeuwenhoek 105 (5)
PMID : 24604690  :   DOI  :   10.1007/s10482-014-0139-y    
Abstract >>
A polyphasic study was carried out to establish the taxonomic status of an Atacama Desert isolate, Streptomyces strain C34(T), which synthesises novel antibiotics, the chaxalactins and chaxamycins. The organism was shown to have chemotaxonomic, cultural and morphological properties consistent with its classification in the genus Streptomyces. Analysis of 16S rRNA gene sequences showed that strain C34(T) formed a distinct phyletic line in the Streptomyces gene tree that was very loosely associated with the type strains of several Streptomyces species. Multilocus sequence analysis based on five house-keeping gene alleles underpinned the separation of strain C34(T) from all of its nearest phylogenetic neighbours, apart from Streptomyces chiangmaiensis TA-1(T) and Streptomyces hyderabadensis OU-40(T) which are not currently in the MLSA database. Strain C34(T) was distinguished readily from the S. chiangmaiensis and S. hyderabadensis strains by using a combination of cultural and phenotypic data. Consequently, strain C34(T) is considered to represent a new species of the genus Streptomyces for which the name Streptomyces leeuwenhoekii sp. nov. is proposed. The type strain is C34(T) (= DSM 42122(T) = NRRL B-24963(T)). Analysis of the whole-genome sequence of S. leeuwenhoekii, with 6,780 predicted open reading frames and a total genome size of around 7.86 Mb, revealed a high potential for natural product biosynthesis.
KeywordMeSH Terms
8. Majumdar  S, Lukk  T, Solbiati  JO, Bauer  S, Nair  SK, Cronan  JE, Gerlt  JA,     ( 2014 )

Roles of small laccases from Streptomyces in lignin degradation.

Biochemistry 53 (24)
PMID : 24870309  :   DOI  :   10.1021/bi500285t    
Abstract >>
Laccases (EC are multicopper oxidases that can oxidize a range of substrates, including phenols, aromatic amines, and nonphenolic substrates. To investigate the involvement of the small Streptomyces laccases in lignin degradation, we generated acid-precipitable polymeric lignin obtained in the presence of wild-type Streptomyces coelicolor A3(2) (SCWT) and its laccase-less mutant (SC�GLAC) in the presence of Miscanthus x giganteus lignocellulose. The results showed that strain SC�GLAC was inefficient in degrading lignin compared to strain SCWT, thereby supporting the importance of laccase for lignin degradation by S. coelicolor A3(2). We also studied the lignin degradation activity of laccases from S. coelicolor A3(2), Streptomyces lividans TK24, Streptomyces viridosporus T7A, and Amycolatopsis sp. 75iv2 using both lignin model compounds and ethanosolv lignin. All four laccases degraded a phenolic model compound (LM-OH) but were able to oxidize a nonphenolic model compound only in the presence of redox mediators. Their activities are highest at pH 8.0 with a low krel/Kapp for LM-OH, suggesting that the enzymes�� natural substrates must be different in shape or chemical nature. Crystal structures of the laccases from S. viridosporus T7A (SVLAC) and Amycolatopsis sp. 75iv2 were determined both with and without bound substrate. This is the first report of a crystal structure for any laccase bound to a nonphenolic �]-O-4 lignin model compound. An additional zinc metal binding site in SVLAC was also identified. The ability to oxidize and/or rearrange ethanosolv lignin provides further evidence of the utility of laccase activity for lignin degradation and/or modification.
KeywordMeSH Terms
9. Ren  F, Ko  TP, Feng  X, Huang  CH, Chan  HC, Hu  Y, Wang  K, Ma  Y, Liang  PH, Wang  AH, Oldfield  E, Guo  RT,     ( 2012 )

Insights into the mechanism of the antibiotic-synthesizing enzyme MoeO5 from crystal structures of different complexes.

Angewandte Chemie (International ed. in English) 51 (17)
PMID : 22431288  :   DOI  :   10.1002/anie.201108002     PMC  :   PMC3454446    
Abstract >>
KeywordMeSH Terms
10.     ( 1996 )

A general approach for cloning and characterizing dNDP-glucose dehydratase genes from actinomycetes.

FEMS microbiology letters 141 (2��3��)
PMID : 8768522  :   DOI  :   10.1111/j.1574-6968.1996.tb08384.x    
Abstract >>
Oligonucleotide primers were designed and successfully applied to amplify DNA fragments of dNDP-glucose dehydratase genes from actinomycete species producing natural compounds which contain deoxysugar moieties. The deduced amino acid sequence of the isolated fragments revealed similarity to known dNDP-glucose dehydratases. A phylogeny for the deduced proteins of the obtained fragments and for dNDP-glucose dehydratases described in the data bases was constructed. dNDP-glucose dehydratases from actinomycetes were more related to each other than to dehydratases from species of other orders. The phylogenetic analysis also revealed a close relation between dehydratases from strains producing natural compounds with similar deoxysugar moieties.
KeywordMeSH Terms
Cloning, Molecular
11. Muth  G, Farr  M, Hartmann  V, Wohlleben  W,     ( 1995 )

Streptomyces ghanaensis plasmid pSG5: nucleotide sequence analysis of the self-transmissible minimal replicon and characterization of the replication mode.

Plasmid 33 (2)
PMID : 7597106  :   DOI  :   10.1006/plas.1995.1013    
Abstract >>
The naturally temperature-sensitive plasmid pSG5 of Streptomyces ghanaensis DSM 2932 is the basis replicon of the "pGM-vectors." The nucleotide sequence of the pSG5 minimal replicon was determined. Only one single open reading frame (rep) with high coding probability is located on the minimal replicon. The deduced Rep protein consists of 378 aa and contains motifs characteristic of initiation proteins for rolling-circle-type replication. Sequence similarity indicated that the Rep protein of pSG5 is related to the Rep proteins of the pC194 plasmid family. Accumulation of large amounts of single-stranded plasmid DNA was shown for all small pGM vectors. A minus origin for the lagging strand synthesis was localized outside of the pSG5 minimal replicon. Although the sequenced pSG5 fragment is self-transmissible, it seems not to carry further genes in addition to the rep gene. This suggests that the transfer mechanism of plasmid pSG5 differs from that of other Streptomyces plasmids, which all encode specific transfer genes.
KeywordMeSH Terms
DNA Helicases
DNA Replication
DNA-Binding Proteins
12. Zhang  L, Ko  TP, Malwal  SR, Liu  W, Zhou  S, Yu  X, Oldfield  E, Guo  RT, Chen  CC,     ( 2019 )

Complex structures of MoeN5 with substrate analogues suggest sequential catalytic mechanism.

Biochemical and biophysical research communications 511 (4)
PMID : 30837154  :   DOI  :   10.1016/j.bbrc.2019.02.131    
Abstract >>
The antibiotic moenomycin A is a phosphoglycerate derivative with a C25-moenocinyl chain and a branched oligosaccharide. Formation of the C25-chain is catalyzed by the enzyme MoeN5 with geranyl pyrophosphate (GPP) and the sugar-linked 2-Z,E-farnesyl-3-phosphoglycerate (FPG) as its substrates. Previous complex crystal structures with GPP and long-chain alkyl glycosides suggested that GPP binds to the S1 site in a similar way as in most other �\-helical prenyltransferases (PTs), and FPG is likely to assume a bent conformation in the S2 site. However, two FPG derivatives synthesized in the current study were found in the S1 site rather than S2 in their complex crystal structures with MoeN5. Apparently S1 is the preferred site for prenyl-containing ligand, and S2 binding may proceed only after S1 is occupied. Thus, like most trans-type PTs, MoeN5 may employ a sequential ionization-condensation-elimination mechanism that involves a carbocation intermediate.
KeywordMeSH Terms
Antibiotics biosynthesis
Sso7d protein tag
X-ray crystallography

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