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1.
Nature ; 629(8010): 165-173, 2024 May.
Article in English | MEDLINE | ID: mdl-38632398

ABSTRACT

Streptomyces are a genus of ubiquitous soil bacteria from which the majority of clinically utilized antibiotics derive1. The production of these antibacterial molecules reflects the relentless competition Streptomyces engage in with other bacteria, including other Streptomyces species1,2. Here we show that in addition to small-molecule antibiotics, Streptomyces produce and secrete antibacterial protein complexes that feature a large, degenerate repeat-containing polymorphic toxin protein. A cryo-electron microscopy structure of these particles reveals an extended stalk topped by a ringed crown comprising the toxin repeats scaffolding five lectin-tipped spokes, which led us to name them umbrella particles. Streptomyces coelicolor encodes three umbrella particles with distinct toxin and lectin composition. Notably, supernatant containing these toxins specifically and potently inhibits the growth of select Streptomyces species from among a diverse collection of bacteria screened. For one target, Streptomyces griseus, inhibition relies on a single toxin and that intoxication manifests as rapid cessation of vegetative hyphal growth. Our data show that Streptomyces umbrella particles mediate competition among vegetative mycelia of related species, a function distinct from small-molecule antibiotics, which are produced at the onset of reproductive growth and act broadly3,4. Sequence analyses suggest that this role of umbrella particles extends beyond Streptomyces, as we identified umbrella loci in nearly 1,000 species across Actinobacteria.


Subject(s)
Antibiosis , Bacterial Proteins , Bacterial Toxins , Streptomyces , Anti-Bacterial Agents/biosynthesis , Anti-Bacterial Agents/chemistry , Anti-Bacterial Agents/metabolism , Anti-Bacterial Agents/pharmacology , Antibiosis/drug effects , Bacterial Proteins/chemistry , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Bacterial Proteins/pharmacology , Bacterial Proteins/ultrastructure , Bacterial Toxins/chemistry , Bacterial Toxins/genetics , Bacterial Toxins/metabolism , Bacterial Toxins/pharmacology , Cryoelectron Microscopy , Lectins/chemistry , Lectins/genetics , Lectins/metabolism , Lectins/ultrastructure , Microbial Sensitivity Tests , Models, Molecular , Streptomyces/chemistry , Streptomyces/drug effects , Streptomyces/genetics , Streptomyces/growth & development , Streptomyces coelicolor/chemistry , Streptomyces coelicolor/genetics , Streptomyces coelicolor/metabolism , Streptomyces griseus/drug effects , Streptomyces griseus/genetics , Streptomyces griseus/growth & development , Streptomyces griseus/metabolism
2.
J Nat Prod ; 87(1): 98-103, 2024 01 26.
Article in English | MEDLINE | ID: mdl-38170464

ABSTRACT

Tetrapetalones make up a unique class of pentaketide ansamycins that feature a tetracyclic skeleton and exhibit potent inhibitory activities against soybean lipoxygenase. However, a detailed biosynthetic route to tetrapetalones has not been published. Herein we report the activation of the tetrapetalones' biosynthetic gene cluster (tpt) in Streptomyces sp. S10 by promoter engineering along with constitutive expression of pathway-specific regulator genes, leading to the discovery of seven new derivatives, tetrapetalones E-K (2-8), and the known tetrapetalone A (1). In vivo gene deletion experiments and heterologous expression of the minimized tpt cluster in Streptomyces albus J1074 suggest that the tetracyclic system of tetrapetalones is probably formed spontaneously, and the regioselective glycosylation of tetrapetalones at the C-9 hydroxy group with d-rhamnose or d-rhodinose was catalyzed by the glycosyltransferase Tpt14.


Subject(s)
Streptomyces griseus , Streptomyces griseus/genetics , Multigene Family , Glycosylation , Glycine max
3.
J Nat Prod ; 86(4): 986-993, 2023 04 28.
Article in English | MEDLINE | ID: mdl-37042607

ABSTRACT

Fidaxomicin (Dificid) is a commercial macrolide antibiotic for treating Clostridium difficile infection. Total synthesis of fidaxomicin and its aglycone had been achieved through different synthetic schemes. In this study, an alternative biological route to afford the unique 18-membered macrolactone aglycone of fidaxomicin was developed. The promoter refactored fidaxomicin biosynthetic gene cluster from Dactylosporangium aurantiacum was expressed in the commonly used host Streptomyces albus J1074, thereby delivering five structurally diverse fidaxomicin aglycones with the corresponding titers ranging from 4.9 to 15.0 mg L-1. In general, these results validated a biological strategy to construct and diversify fidaxomicin aglycones on the basis of promoter refactoring and heterologous expression.


Subject(s)
Anti-Bacterial Agents , Streptomyces griseus , Fidaxomicin , Macrolides/metabolism , Streptomyces griseus/genetics , Multigene Family , Aminoglycosides
4.
Chembiochem ; 23(3): e202100517, 2022 02 04.
Article in English | MEDLINE | ID: mdl-34767291

ABSTRACT

Indolizidine alkaloids, which have versatile bioactivities, are produced by various organisms. Although the biosynthesis of some indolizidine alkaloids has been studied, the enzymatic machinery for their biosynthesis in Streptomyces remains elusive. Here, we report the identification and analysis of the biosynthetic gene cluster for iminimycin, an indolizidine alkaloid with a 6-5-3 tricyclic system containing an iminium cation from Streptomyces griseus. The gene cluster has 22 genes, including four genes encoding polyketide synthases (PKSs), which consist of eight modules in total. In vitro analysis of the first module revealed that its acyltransferase domain selects malonyl-CoA, although predicted to select methylmalonyl-CoA. Inactivation of seven tailoring enzyme-encoding genes and structural elucidation of four compounds accumulated in mutants provided important insights into iminimycin biosynthesis, although some of these compounds appeared to be shunt products. This study expands our knowledge of the biosynthetic machinery of indolizidine alkaloids and the enzymatic chemistry of PKS.


Subject(s)
Alkaloids/biosynthesis , Multigene Family , Streptomyces griseus/chemistry , Streptomyces griseus/genetics , Alkaloids/chemistry , Indolizidines/chemistry , Molecular Conformation , Streptomyces griseus/metabolism
5.
J Virol ; 93(5)2019 03 01.
Article in English | MEDLINE | ID: mdl-30518649

ABSTRACT

Here, we investigate an unusual antiviral mechanism developed in the bacterium Streptomyces griseus SgrAI is a type II restriction endonuclease that forms run-on oligomer filaments when activated and possesses both accelerated DNA cleavage activity and expanded DNA sequence specificity. Mutations disrupting the run-on oligomer filament eliminate the robust antiphage activity of wild-type SgrAI, and the observation that even relatively modest disruptions completely abolish this anti-viral activity shows that the greater speed imparted by the run-on oligomer filament mechanism is critical to its biological function. Simulations of DNA cleavage by SgrAI uncover the origins of the kinetic advantage of this newly described mechanism of enzyme regulation over more conventional mechanisms, as well as the origin of the sequestering effect responsible for the protection of the host genome against damaging DNA cleavage activity of activated SgrAI.IMPORTANCE This work is motivated by an interest in understanding the characteristics and advantages of a relatively newly discovered enzyme mechanism involving filament formation. SgrAI is an enzyme responsible for protecting against viral infections in its host bacterium and was one of the first such enzymes shown to utilize such a mechanism. In this work, filament formation by SgrAI is disrupted, and the effects on the speed of the purified enzyme as well as its function in cells are measured. It was found that even small disruptions, which weaken but do not destroy filament formation, eliminate the ability of SgrAI to protect cells from viral infection, its normal biological function. Simulations of enzyme activity were also performed and show how filament formation can greatly speed up an enzyme's activation compared to that of other known mechanisms, as well as to better localize its action to molecules of interest, such as invading phage DNA.


Subject(s)
Bacteriophages/genetics , DNA, Viral/metabolism , Deoxyribonucleases, Type II Site-Specific/metabolism , Streptomyces griseus/virology , Bacteriophages/growth & development , Base Sequence/genetics , DNA, Viral/genetics , Deoxyribonucleases, Type II Site-Specific/genetics , Enzyme Activation , Streptomyces griseus/genetics , Structure-Activity Relationship , Substrate Specificity
6.
Biosci Biotechnol Biochem ; 83(11): 2082-2089, 2019 Nov.
Article in English | MEDLINE | ID: mdl-31303144

ABSTRACT

Frigocyclinone is a novel antibiotic with antibacterial and anticancer activities. It is produced by both Antarctica-derived Streptomyces griseus NTK 97 and marine sponge-associated Streptomyces sp. M7_15. Here, we first report the biosynthetic gene cluster of frigocyclinone in the S. griseus NTK 97. The frigocyclinone gene cluster spans a DNA region of 33-kb which consists of 30 open reading frames (ORFs), encoding minimal type II polyketide synthase, aromatase and cyclase, redox tailoring enzymes, sugar biosynthesis-related enzymes, C-glycosyltransferase, a resistance protein, and three regulatory proteins. Based on the bioinformatic analysis, a biosynthetic pathway for frigocyclinone was proposed. Second, to verify the cloned gene cluster, CRISPR-Cpf1 mediated gene disruption was conducted. Mutant with the disruption of beta-ketoacyl synthase encoding gene frig20 fully loses the ability of producing frigocyclinone, while inactivating the glycosyltransferase gene frig1 leads to the production of key intermediate of anti-MRSA anthraquinone tetrangomycin.


Subject(s)
Anthraquinones/metabolism , Multigene Family/genetics , Streptomyces griseus/genetics , Streptomyces griseus/metabolism , Cloning, Molecular , Glycosyltransferases/genetics , Glycosyltransferases/metabolism , Streptomyces griseus/enzymology
7.
J Nat Prod ; 81(1): 72-77, 2018 01 26.
Article in English | MEDLINE | ID: mdl-29338229

ABSTRACT

Diazofluorene compounds such as kinamycin and lomaiviticin feature unique molecular structures and compelling medicinal bioactivities. However, a complete understanding of the biosynthetic details for this family of natural products has yet to be fully elucidated. In addition, a lack of genetically and technically amenable production hosts has limited access to the full medicinal potential of these compounds. Here, we report the capture of the complete kinamycin gene cluster from Streptomyces galtieri Sgt26 by bacterial artificial chromosome cloning, confirmed by successful production of kinamycin in the heterologous host Streptomyces albus J1074. Sequence analysis and a series of gene deletion experiments revealed the boundary of the cluster, which spans 75 kb DNA. To probe the last step in biosynthesis, acetylation of kinamcyin F to kinamycin D, gene knockout, and complementation experiments identified a single gene product involved with final acetylation conversions. This study provides full genetic information for the kinamycin gene cluster from S. galtieri Sgt26 and establishes heterologous biosynthesis as a production platform for continued mechanistic assessment of compound formation and utilization.


Subject(s)
Biological Products/metabolism , Streptomyces griseus/genetics , Gene Deletion , Multigene Family/genetics
8.
Proc Natl Acad Sci U S A ; 112(9): 2717-22, 2015 Mar 03.
Article in English | MEDLINE | ID: mdl-25730866

ABSTRACT

The bacterial tryptophanyl-tRNA synthetase inhibitor indolmycin features a unique oxazolinone heterocycle whose biogenetic origins have remained obscure for over 50 years. Here we identify and characterize the indolmycin biosynthetic pathway, using systematic in vivo gene inactivation, in vitro biochemical assays, and total enzymatic synthesis. Our work reveals that a phenylacetate-CoA ligase-like enzyme Ind3 catalyzes an unusual ATP-dependent condensation of indolmycenic acid and dehydroarginine, driving oxazolinone ring assembly. We find that Ind6, which also has chaperone-like properties, acts as a gatekeeper to direct the outcome of this reaction. With Ind6 present, the normal pathway ensues. Without Ind6, the pathway derails to an unusual shunt product. Our work reveals the complete pathway for indolmycin formation and sets the stage for using genetic and chemoenzymatic methods to generate indolmycin derivatives as potential therapeutic agents.


Subject(s)
Bacterial Proteins/metabolism , Escherichia coli/metabolism , Oxazolone/analogs & derivatives , Rhodococcus/metabolism , Streptomyces griseus/metabolism , Bacterial Proteins/genetics , Base Sequence , Cell-Free System/metabolism , Coenzyme A Ligases/genetics , Coenzyme A Ligases/metabolism , Escherichia coli/genetics , Indoles/metabolism , Molecular Chaperones/genetics , Molecular Chaperones/metabolism , Molecular Sequence Data , Oxazolone/metabolism , Rhodococcus/genetics , Streptomyces griseus/genetics
9.
J Biol Chem ; 291(16): 8618-31, 2016 Apr 15.
Article in English | MEDLINE | ID: mdl-26921320

ABSTRACT

Isoleucyl-tRNA synthetase (IleRS) is unusual among aminoacyl-tRNA synthetases in having a tRNA-dependent pre-transfer editing activity. Alongside the typical bacterial IleRS (such as Escherichia coli IleRS), some bacteria also have the enzymes (eukaryote-like) that cluster with eukaryotic IleRSs and exhibit low sensitivity to the antibiotic mupirocin. Our phylogenetic analysis suggests that the ileS1 and ileS2 genes of contemporary bacteria are the descendants of genes that might have arisen by an ancient duplication event before the separation of bacteria and archaea. We present the analysis of evolutionary constraints of the synthetic and editing reactions in eukaryotic/eukaryote-like IleRSs, which share a common origin but diverged through adaptation to different cell environments. The enzyme from the yeast cytosol exhibits tRNA-dependent pre-transfer editing analogous to E. coli IleRS. This argues for the presence of this proofreading in the common ancestor of both IleRS types and an ancient origin of the synthetic site-based quality control step. Yet surprisingly, the eukaryote-like enzyme from Streptomyces griseus IleRS lacks this capacity; at the same time, its synthetic site displays the 10(3)-fold drop in sensitivity to antibiotic mupirocin relative to the yeast enzyme. The discovery that pre-transfer editing is optional in IleRSs lends support to the notion that the conserved post-transfer editing domain is the main checkpoint in these enzymes. We substantiated this by showing that under error-prone conditions S. griseus IleRS is able to rescue the growth of an E. coli lacking functional IleRS, providing the first evidence that tRNA-dependent pre-transfer editing in IleRS is not essential for cell viability.


Subject(s)
Isoleucine-tRNA Ligase/metabolism , RNA, Transfer/metabolism , Streptomyces griseus/enzymology , Escherichia coli/enzymology , Escherichia coli/genetics , Genetic Complementation Test , Isoleucine-tRNA Ligase/genetics , RNA, Transfer/genetics , Streptomyces griseus/genetics
10.
Anal Chem ; 89(20): 10744-10752, 2017 10 17.
Article in English | MEDLINE | ID: mdl-28942636

ABSTRACT

Liquid chromatography tandem mass spectrometry (LC-MS/MS) has proven to be a powerful analytical tool for the characterization of modified ribonucleic acids (RNAs). The typical approach for analyzing modified nucleosides within RNA sequences by mass spectrometry involves ribonuclease digestion followed by LC-MS/MS analysis and data interpretation. Here we describe a new software tool, RNAModMapper (RAMM), to assist in the interpretation of LC-MS/MS data. RAMM is a stand-alone package that requires user-submitted DNA or RNA sequences to create a local database against which collision-induced dissociation (CID) data of modified oligonucleotides can be compared. RAMM can interpret MS/MS data containing modified nucleosides in two modes: fixed and variable. In addition, RAMM can also utilize interpreted MS/MS data for RNA modification mapping back against the input sequence(s). The applicability of RAMM was first tested using total tRNA isolated from Escherichia coli. It was then applied to map modifications found in 16S and 23S rRNA from Streptomyces griseus.


Subject(s)
RNA/analysis , Software , Tandem Mass Spectrometry , Area Under Curve , Chromatography, High Pressure Liquid , Databases, Factual , Nucleosides/chemistry , RNA/metabolism , RNA, Ribosomal, 16S/analysis , RNA, Ribosomal, 16S/metabolism , RNA, Ribosomal, 23S/analysis , RNA, Ribosomal, 23S/metabolism , ROC Curve , Ribonuclease T1/metabolism , Streptomyces griseus/genetics
11.
Protein Expr Purif ; 132: 164-170, 2017 04.
Article in English | MEDLINE | ID: mdl-28161545

ABSTRACT

A novel ß-glucosidase from Streptomyces griseus was cloned and overexpressed in E. coli. The purified ß-glucosidase (44 kDa) had a Km of 8.6 ± 0.5 mM and a Vmax of 217 ± 5.0 µmoles-1min-1mg at 37 °C, pH 7.2 with p-nitrophenyl-ß-D glucopyranoside as substrate. The enzyme was characterised in terms of pH optimum (pH 6.9), temperature optimum (69 °C) and the influence of solvents and effectors. Purified S. griseus ß-glucosidase was successfully immobilised, by simple absorption, onto zinc oxide (ZnO) nanoparticles without covalent modification. It remained tightly bound even after extensive washing and could be reused up to ten times without significant loss of activity. The immobilised enzyme had a higher optimum temperature and greater thermostability than the free enzyme. In immobilised form the enzyme readily catalysed the synthesis of alkyl glucosides.


Subject(s)
Bacterial Proteins , Glucosides/chemical synthesis , Nanoparticles/chemistry , Streptomyces griseus/genetics , beta-Glucosidase , Bacterial Proteins/biosynthesis , Bacterial Proteins/chemistry , Bacterial Proteins/genetics , Bacterial Proteins/isolation & purification , Glucosides/chemistry , Recombinant Proteins/biosynthesis , Recombinant Proteins/chemistry , Recombinant Proteins/genetics , Recombinant Proteins/isolation & purification , Streptomyces griseus/enzymology , beta-Glucosidase/biosynthesis , beta-Glucosidase/chemistry , beta-Glucosidase/genetics , beta-Glucosidase/isolation & purification
12.
Biosci Biotechnol Biochem ; 81(1): 153-164, 2017 Jan.
Article in English | MEDLINE | ID: mdl-27691921

ABSTRACT

AmfS, a class III lantipeptide serves as a morphogen in Streptomyces griseus. Here, we constructed a high production system of AmfS in S. griseus. We isolated S. griseus Grd1 strain defective in glucose repression of aerial mycelium formation and found it suitable for the overproduction of AmfS. Two expression vectors carrying the strong and constitutive ermE2 promoter were constructed using a multicopy number plasmid, pIJ702. The use of the Grd1 strain combined with the expression vectors enabled high production of AmfS by S. griseus into its culture broth. The expression system was also effective for the generation of abundant AmfS derived from Streptomyces avermitilis. In addition, site-directed mutagenesis revealed the amino acid residues essential for the morphogen activity of AmfS. These results indicate that the constructed system enables efficient production of class III lantipeptides by Streptomyces.


Subject(s)
Bacterial Proteins/biosynthesis , Genetic Engineering , Streptomyces griseus/genetics , Streptomyces griseus/metabolism , Amino Acid Sequence , Bacterial Proteins/chemistry , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Genetic Vectors/genetics , Multigene Family/genetics , Mutation
13.
World J Microbiol Biotechnol ; 33(5): 82, 2017 May.
Article in English | MEDLINE | ID: mdl-28378221

ABSTRACT

In order to produce enantiomerically pure epoxides for the synthesis of value-added chemicals, a novel putative epoxide hydrolase (EH) sgeh was cloned and overexpressed in pET28a/Escherichia coli BL21(DE3). The 1047 bp sgeh gene was mined from Streptomyces griseus NBRC 13350 genome sequence. The recombinant hexahistidyl-tagged SGEH was purified (16.6-fold) by immobilized metal-affinity chromatography, with 90% yield as a homodimer of 100 kDa. The recombinant E. coli whole cells overexpressing SGEH could kinetically resolve racemic phenyl glycidyl ether (PGE) into (R)-PGE with 98% ee, 40% yield, and enantiomeric ratio (E) of 20. This was achieved under the optimized reaction conditions i.e. cell/substrate ratio of 20:1 (w/w) at pH 7.5 and 20 °C in 10% (v/v) dimethylformamide (DMF) in a 10 h reaction. 99% enantiopure (R)-PGE was obtained when the reaction time was prolonged to 12 h with a yield of 34%. In conclusion, an economically viable and environment friendly green process for the production of enantiopure (R)-PGE was developed by using wet cells of E. coli expressing recombinant SGEH.


Subject(s)
Epoxide Hydrolases/metabolism , Phenyl Ethers/metabolism , Streptomyces griseus/enzymology , Chromatography, Gel , Cloning, Molecular , Epoxide Hydrolases/genetics , Escherichia coli/genetics , Kinetics , Recombinant Proteins/metabolism , Stereoisomerism , Streptomyces griseus/genetics , Substrate Specificity
14.
Appl Environ Microbiol ; 82(2): 467-77, 2016 01 15.
Article in English | MEDLINE | ID: mdl-26519385

ABSTRACT

Albomycin (ABM), also known as grisein, is a sulfur-containing metabolite produced by Streptomyces griseus ATCC 700974. Genes predicted to be involved in the biosynthesis of ABM and ABM-like molecules are found in the genomes of other actinomycetes. ABM has potent antibacterial activity, and as a result, many attempts have been made to develop ABM into a drug since the last century. Although the productivity of S. griseus can be increased with random mutagenesis methods, understanding of Streptomyces sulfur amino acid (SAA) metabolism, which supplies a precursor for ABM biosynthesis, could lead to improved and stable production. We previously characterized the gene cluster (abm) in the genome-sequenced S. griseus strain and proposed that the sulfur atom of ABM is derived from either cysteine (Cys) or homocysteine (Hcy). The gene product, AbmD, appears to be an important link between primary and secondary sulfur metabolic pathways. Here, we show that propargylglycine or iron supplementation in growth media increased ABM production by significantly changing the relative concentrations of intracellular Cys and Hcy. An SAA metabolic network of S. griseus was constructed. Pathways toward increasing Hcy were shown to positively impact ABM production. The abmD gene and five genes that increased the Hcy/Cys ratio were assembled downstream of hrdBp promoter sequences and integrated into the chromosome for overexpression. The ABM titer of one engineered strain, SCAK3, in a chemically defined medium was consistently improved to levels ∼400% of the wild type. Finally, we analyzed the production and growth of SCAK3 in shake flasks for further process development.


Subject(s)
Amino Acids, Sulfur/metabolism , Anti-Bacterial Agents/biosynthesis , Ferrichrome/analogs & derivatives , Streptomyces griseus/metabolism , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Ferrichrome/metabolism , Multigene Family , Streptomyces griseus/genetics , Streptomyces griseus/growth & development
15.
Anal Chem ; 87(16): 8433-40, 2015 Aug 18.
Article in English | MEDLINE | ID: mdl-26176336

ABSTRACT

There has been a renewed appreciation for the dynamic nature of ribonucleic acid (RNA) modifications and for the impact of modified RNAs on organism health resulting in an increased emphasis on developing analytical methods capable of detecting modifications within specific RNA sequence contexts. Here we demonstrate that a DNA-based exclusion list enhances data dependent liquid chromatography tandem mass spectrometry (LC-MS/MS) detection of post-transcriptionally modified nucleosides within specific RNA sequences. This approach is possible because all post-transcriptional modifications of RNA, except pseudouridine, result in a mass increase in the canonical nucleoside undergoing chemical modification. Thus, DNA-based sequences reflect the state of the RNA prior to or in the absence of modification. The utility of this exclusion list strategy is demonstrated through the RNA modification mapping of total tRNAs from the bacteria Escherichia coli, Lactococcus lactis, and Streptomyces griseus. Creation of a DNA-based exclusion list is shown to consistently enhance the number of detected modified ribonuclease (RNase) digestion products by ∼20%. All modified RNase digestion products that were detected during standard data dependent acquisition (DDA) LC-MS/MS were also detected when the DNA-based exclusion list was used. Consequently, the increase in detected modified RNase digestion products is attributed to new experimental information only obtained when using the exclusion list. This exclusion list strategy should be broadly applicable to any class of RNA and improves the utility of mass spectrometry approaches for discovery-based analyses of RNA modifications, such as are required for studies of the epitranscriptome.


Subject(s)
RNA, Bacterial/analysis , RNA, Transfer/analysis , Tandem Mass Spectrometry , Chromatography, High Pressure Liquid , Escherichia coli/genetics , Lactococcus lactis/genetics , RNA, Bacterial/metabolism , RNA, Bacterial/standards , RNA, Transfer/metabolism , RNA, Transfer/standards , Ribonucleases/metabolism , Streptomyces griseus/genetics , Tandem Mass Spectrometry/standards
16.
J Bacteriol ; 196(7): 1369-76, 2014 Apr.
Article in English | MEDLINE | ID: mdl-24443533

ABSTRACT

The glycine cleavage (GCV) system catalyzes the oxidative cleavage of glycine into CO2, NH4(+), and a methylene group, which is accepted by tetrahydrofolate (THF) to form N(5),N(10)-methylene-THF. Streptomyces griseus contains gcvP and the gcvT-gcvH operon, which encode three intrinsic components of the GCV system. We identified the transcriptional start sites of gcvTH and gcvP and found putative glycine riboswitches in their 5' untranslated regions (5' UTRs). The ratios of the transcripts of the gcvT and gcvP coding sequences (CDSs) to those of the respective 5' UTRs were significantly higher in the presence of glycine in the wild-type strain. However, the levels of gcvT and gcvP CDS transcripts were not increased by glycine in the respective 5' UTR deletion mutants. A reporter gene assay showed that a transcriptional terminator exists in the 5' UTR of gcvTH. Furthermore, by an in-line probing assay, we confirmed that glycine bound directly to the putative riboswitch RNAs. These results indicate that the S. griseus glycine riboswitches enhance transcriptional read-through to the downstream CDSs, like known glycine riboswitches in other bacteria. We examined the growth of three mutants in which either or both of the gcvTH and gcvP 5' UTRs were deleted. Like the wild-type strain, all mutants grew vigorously in a medium containing 0.9% glucose as a carbon source. However, the mutants showed severely restricted growth in a medium containing 0.9% glucose and 1% glycine, while the wild-type strain grew normally. This indicates that glycine has a growth-inhibitory effect and that the GCV system plays a critical role in glycine detoxification in S. griseus.


Subject(s)
Amino Acid Oxidoreductases/genetics , Bacterial Proteins/genetics , Carrier Proteins/genetics , Gene Expression Regulation, Enzymologic , Glycine/metabolism , Multienzyme Complexes/genetics , RNA, Bacterial/genetics , Riboswitch , Streptomyces griseus/enzymology , Transcriptional Activation , Transferases/genetics , 5' Untranslated Regions , Amino Acid Oxidoreductases/metabolism , Bacterial Proteins/metabolism , Base Sequence , Carrier Proteins/metabolism , Gene Expression Regulation, Bacterial , Molecular Sequence Data , Multienzyme Complexes/metabolism , Operon , RNA, Bacterial/metabolism , Streptomyces griseus/genetics , Streptomyces griseus/metabolism , Transferases/metabolism , Up-Regulation
17.
J Biol Chem ; 288(43): 31019-29, 2013 Oct 25.
Article in English | MEDLINE | ID: mdl-24019524

ABSTRACT

AdpA serves as the global transcription factor in the A-factor regulatory cascade, controlling the secondary metabolism and morphological differentiation of the filamentous bacterium Streptomyces griseus. AdpA binds to over 500 operator regions with the consensus sequence 5'-TGGCSNGWWY-3' (where S is G or C, W is A or T, Y is T or C, and N is any nucleotide). However, it is still obscure how AdpA can control hundreds of genes. To elucidate the structural basis of this tolerant DNA recognition by AdpA, we focused on the interaction between the DNA-binding domain of AdpA (AdpA-DBD), which consists of two helix-turn-helix motifs, and a target duplex DNA containing the consensus sequence 5'-TGGCGGGTTC-3'. The crystal structure of the AdpA-DBD-DNA complex and the mutant analysis of AdpA-DBD revealed its unique manner of DNA recognition, whereby only two arginine residues directly recognize the consensus sequence, explaining the strict recognition of G and C at positions 2 and 4, respectively, and the tolerant recognition of other positions of the consensus sequence. AdpA-DBD confers tolerant DNA sequence specificity to AdpA, allowing it to control hundreds of genes as a global transcription factor.


Subject(s)
Bacterial Proteins/chemistry , DNA, Bacterial/chemistry , Response Elements , Streptomyces griseus/chemistry , Trans-Activators/chemistry , Bacterial Proteins/genetics , Crystallography, X-Ray , DNA, Bacterial/genetics , Protein Structure, Tertiary , Streptomyces griseus/genetics , Trans-Activators/genetics
18.
Mol Microbiol ; 87(6): 1223-36, 2013 Mar.
Article in English | MEDLINE | ID: mdl-23347076

ABSTRACT

In bacteria, the RNA polymerase holoenzyme comprises a five-subunit core enzyme and a dissociable subunit, sigma factor, which is responsible for transcriptional initiation. The filamentous bacterium Streptomyces griseus has 52 sigma factors, including one essential 'principal' sigma factor (σ(HrdB) ) that is responsible for the transcription of housekeeping genes. Here we characterized an alternative sigma factor (σ(ShbA) ), which is highly conserved within the genus Streptomyces. A σ(ShbA) -deficient mutant showed a severe growth defect and transcriptome analysis indicated that many housekeeping genes were downregulated in response to insufficient σ(ShbA) production. Biochemical and genetic analyses proved that σ(ShbA) is a major determinant of transcription of the σ(HrdB) gene. This observation of a principal sigma factor being governed by another sigma factor throughout growth is unprecedented. We found that increasing σ(ShbA) production with mycelial growth maintained a high σ(HrdB) level late in growth. Furthermore, a hrdB-autoregulatable σ(ShbA) -deficient mutant, in which the principal sigma factor gene can be transcribed by RNA polymerase containing σ(HrdB) itself, showed several defects: rapid mycelial lysis in stationary phase in liquid culture and delayed morphological development and impaired streptomycin production in solid culture. From these observations, we discuss the biological significance of control of σ(HrdB) by σ(ShbA) in S. griseus.


Subject(s)
Gene Expression Regulation, Bacterial , Sigma Factor/metabolism , Streptomyces griseus/genetics , Gene Deletion , Gene Expression Profiling , Sigma Factor/genetics , Streptomyces griseus/growth & development , Streptomyces griseus/metabolism
19.
Appl Environ Microbiol ; 80(4): 1371-9, 2014 Feb.
Article in English | MEDLINE | ID: mdl-24334658

ABSTRACT

Cytochrome P450 monooxygenases (P450s), which constitute a superfamily of heme-containing proteins, catalyze the direct oxidation of a variety of compounds in a regio- and stereospecific manner; therefore, they are promising catalysts for use in the oxyfunctionalization of chemicals. In the course of our comprehensive substrate screening for all 27 putative P450s encoded by the Streptomyces griseus genome, we found that Escherichia coli cells producing an S. griseus P450 (CYP154C3), which was fused C terminally with the P450 reductase domain (RED) of a self-sufficient P450 from Rhodococcus sp., could transform various steroids (testosterone, progesterone, Δ(4)-androstene-3,17-dione, adrenosterone, 1,4-androstadiene-3,17-dione, dehydroepiandrosterone, 4-pregnane-3,11,20-trione, and deoxycorticosterone) into their 16α-hydroxy derivatives as determined by nuclear magnetic resonance and high-resolution mass spectrometry analyses. The purified CYP154C3, which was not fused with RED, also catalyzed the regio- and stereospecific hydroxylation of these steroids at the same position with the aid of ferredoxin and ferredoxin reductase from spinach. The apparent equilibrium dissociation constant (Kd) values of the binding between CYP154C3 and these steroids were less than 8 µM as determined by the heme spectral change, indicating that CYP154C3 strongly binds to these steroids. Furthermore, kinetic parameters of the CYP154C3-catalyzed hydroxylation of Δ(4)-androstene-3,17-dione were determined (Km, 31.9 ± 9.1 µM; kcat, 181 ± 4.5 s(-1)). We concluded that CYP154C3 is a steroid D-ring 16α-specific hydroxylase which has considerable potential for industrial applications. This is the first detailed enzymatic characterization of a P450 enzyme that has a steroid D-ring 16α-specific hydroxylation activity.


Subject(s)
Cytochrome P-450 Enzyme System/metabolism , Steroids/metabolism , Streptomyces griseus/enzymology , Cytochrome P-450 Enzyme System/genetics , Escherichia coli/genetics , Escherichia coli/metabolism , Hydroxylation , Kinetics , Magnetic Resonance Spectroscopy , Mass Spectrometry , Recombinant Proteins/genetics , Recombinant Proteins/metabolism , Streptomyces griseus/genetics
20.
World J Microbiol Biotechnol ; 30(6): 1819-27, 2014 Jun.
Article in English | MEDLINE | ID: mdl-24458877

ABSTRACT

Streptomyces trypsin is one of the serine proteinases in Streptomyces griseus and acts as a key mediator during cell growth and differentiation. S. griseus trypsin (SGT) could be successfully expressed in Pichia pastoris by engineering the natural propeptide APNP. In this study, the recombinant Exmt with peptide YVEF and the wild-type SGT were comparatively investigated in detail. The recombinant Exmt showed significantly increased thermostability which t(½) value was 3.89-fold of that of the SGT at 40 °C. Moreover, the catalytic efficiency (referring to the specificity constant, k cat/K m) and pH tolerance of Exmt were also improved. In silico modeling analysis uncovered that introduction of the peptide YVEF resulted in a broadened substrate binding pocket and closer catalytic triad (His57, Asp¹°² and Ser¹95). The intramolecular Hydrogen bonds and the cation π-interactions were also dramatically increased. The results indicated that engineering of the N-terminus with artificial peptides might be an effective approach for optimizing the properties of the target enzymes.


Subject(s)
Bacterial Proteins/chemistry , Bacterial Proteins/genetics , Peptides/genetics , Protein Engineering , Streptomyces griseus/enzymology , Trypsin/chemistry , Trypsin/genetics , Amino Acid Motifs , Bacterial Proteins/metabolism , Biocatalysis , Enzyme Stability , Kinetics , Peptides/metabolism , Recombinant Fusion Proteins/chemistry , Recombinant Fusion Proteins/genetics , Recombinant Fusion Proteins/metabolism , Streptomyces griseus/chemistry , Streptomyces griseus/genetics , Trypsin/metabolism
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