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1.
J Bacteriol ; 192(23): 6317-8, 2010 Dec.
Article in English | MEDLINE | ID: mdl-20889745

ABSTRACT

Streptomyces clavuligerus is an important industrial strain that produces a number of antibiotics, including clavulanic acid and cephamycin C. A high-quality draft genome sequence of the S. clavuligerus NRRL 3585 strain was produced by employing a hybrid approach that involved Sanger sequencing, Roche/454 pyrosequencing, optical mapping, and partial finishing. Its genome, comprising four linear replicons, one chromosome, and four plasmids, carries numerous sets of genes involved in the biosynthesis of secondary metabolites, including a variety of antibiotics.


Subject(s)
DNA, Bacterial/chemistry , DNA, Bacterial/genetics , Genome, Bacterial , Streptomyces/genetics , Biosynthetic Pathways/genetics , Chromosomes, Bacterial , Molecular Sequence Data , Plasmids , Sequence Analysis, DNA/methods
2.
Appl Microbiol Biotechnol ; 88(3): 659-69, 2010 Oct.
Article in English | MEDLINE | ID: mdl-20711575

ABSTRACT

Clavulanic acid, a ß-lactamase inhibitor, is used together with ß-lactam antibiotics to create drug mixtures possessing potent antimicrobial activity. In view of the clinical and industrial importance of clavulanic acid, identification of the clavulanic acid biosynthetic pathway and the associated gene cluster(s) in the main producer species, Streptomyces clavuligerus, has been an intriguing research question. Clavulanic acid biosynthesis was revealed to involve an interesting mechanism common to all of the clavam metabolites produced by the organism, but different from that of other ß-lactam compounds. Gene clusters involved in clavulanic acid biosynthesis in S. clavuligerus occupy large regions of nucleotide sequence in three loci of its genome. In this review, clavulanic acid biosynthesis and the associated gene clusters are discussed, and clavulanic acid improvement through genetic manipulation is explained.


Subject(s)
Anti-Bacterial Agents/biosynthesis , Clavulanic Acid/biosynthesis , Clavulanic Acids/biosynthesis , Genetic Engineering/methods , Streptomyces/genetics , Genes, Bacterial , Molecular Structure , Multigene Family , Streptomyces/metabolism , beta-Lactamases/biosynthesis , beta-Lactamases/genetics
3.
FEMS Microbiol Rev ; 34(2): 171-98, 2010 Mar.
Article in English | MEDLINE | ID: mdl-20088961

ABSTRACT

Streptomycetes, soil-dwelling mycelial bacteria that form sporulating aerial branches, have an exceptionally large number of predicted secreted proteins, including many exported via the twin-arginine transport system. Their use of noncatalytic substrate-binding proteins and hydrolytic enzymes to obtain soluble nutrients from carbohydrates such as chitin and cellulose enables them to interact with other organisms. Some of their numerous secreted proteases participate in developmentally significant extracellular cascades, regulated by inhibitors, which lead to cannibalization of the substrate mycelium biomass to support aerial growth and sporulation. They excrete many secondary metabolites, including important antibiotics. Some of these play roles in interactions with eukaryotes. Surprisingly, some antibiotic biosynthetic enzymes are extracellular. Antibiotic production is often regulated by extracellular signalling molecules, some of which also control morphological differentiation. Amphipathic proteins, assembled with the help of cellulose-like material, are required for both hyphal attachment to surfaces and aerial reproductive growth. Comparative genomic analysis suggests that the acquisition of genes for extracellular processes has played a huge part in speciation. The rare codon TTA, which is present in the key pleiotropic regulatory gene adpA and many pathway-specific regulatory genes for antibiotic production, has a particular influence on extracellular biology.


Subject(s)
Bacterial Proteins/metabolism , Streptomyces/physiology , Anti-Bacterial Agents/metabolism , Enzymes/metabolism , Evolution, Molecular , Genome, Bacterial , Protein Binding , Protein Transport , Streptomyces/genetics , Streptomyces/metabolism
4.
J Mol Biol ; 389(2): 289-305, 2009 Jun 05.
Article in English | MEDLINE | ID: mdl-19332077

ABSTRACT

Beta-lactamase inhibitory protein (BLIP) binds a variety of beta-lactamase enzymes with wide-ranging specificity. Its binding mechanism and interface interactions are a well-established model system for the characterization of protein-protein interactions. Published studies have examined the binding of BLIP to diverse target beta-lactamases (e.g., TEM-1, SME-1, and SHV-1). However, apart from point mutations of amino acid residues, variability on the inhibitor side of this enzyme-inhibitor interface has remained unexplored. Thus, we present crystal structures of two likely BLIP relatives: (1) BLIP-I (solved alone and in complex with TEM-1), which has beta-lactamase inhibitory activity very similar to that of BLIP; and (2) beta-lactamase-inhibitory-protein-like protein (BLP) (in two apo forms, including an ultra-high-resolution structure), which is unable to inhibit any tested beta-lactamase. Despite categorical differences in species of origin and function, BLIP-I and BLP share nearly identical backbone conformations, even at loop regions differing in BLIP. We describe interacting residues and provide a comparative structural analysis of the interactions formed at the interface of BLIP-I.TEM-1 versus those formed at the interface of BLIP.TEM-1. Along with initial attempts to functionally characterize BLP, we examine its amino acid residues that structurally correspond to BLIP/BLIP-I binding hotspots to explain its inability to bind and inhibit TEM-1. We conclude that the BLIP family fold is a robust and flexible scaffold that permits the formation of high-affinity protein-protein interactions while remaining highly selective. Comparison of the two naturally occurring, distinct binding interfaces built upon this scaffold (BLIP and BLIP-I) shows that there is substantial variation possible in the subnanomolar binding interaction with TEM-1. The corresponding (non-TEM-1-binding) BLP surface shows that numerous favorable backbone-backbone/backbone-side-chain interactions with a protein partner can be negated by the presence of a few, strongly unfavorable interactions, especially electrostatic repulsions.


Subject(s)
Bacterial Proteins/chemistry , beta-Lactamase Inhibitors , Amino Acids , Binding Sites , Crystallography, X-Ray , Protein Binding , Static Electricity , beta-Lactamases/chemistry
5.
J Ind Microbiol Biotechnol ; 36(2): 301-11, 2009 Feb.
Article in English | MEDLINE | ID: mdl-19011915

ABSTRACT

Three open reading frames denoted as orf21, orf22, and orf23 were identified from downstream of the currently recognized gene cluster for clavulanic acid biosynthesis in Streptomyces clavuligerus ATCC 27064. The new orfs were annotated after in silico analysis as genes encoding a putative sigma factor, a sensor kinase, and a response regulator. The roles of the individual genes were explored by disruption of the corresponding orfs, and the morphological and antibiotic production phenotypes of the resulting mutants were compared. In orf21 and orf22 mutants, no growth or morphological differences were noted, but modest reduction of cephamycin C (orf21), or both cephamycin C and clavulanic acid production (orf22) compared with wild-type, were observed. In orf23 mutant, cell growth and sporulation was retarded, and clavulanic acid and cephamycin C production were reduced to 40 and 47% of wild-type levels, respectively. Conversely, overexpression of orf23 caused precocious hyperproduction of spores on solid medium, and antibiotic production was increased above the levels seen in plasmid control cultures. Transcriptional analyses were also carried out on orf23 and showed that mutation had little effect on transcription of genes associated with the early stages of cephamycin C or clavulanic acid production but transcription of claR, which regulates the late stages of clavulanic acid production, was reduced in orf23 mutants. These observations suggest that the orf23 product may enable S. clavuligerus to respond to environmental changes by altering cell growth and differentiation. In addition, the effects of ORF23 on growth might indirectly regulate the biosynthesis of secondary metabolites such as clavulanic acid and cephamycin C.


Subject(s)
Bacterial Proteins/genetics , Clavulanic Acid/biosynthesis , Gene Expression Regulation, Bacterial , Multigene Family , Streptomyces/metabolism , Anti-Bacterial Agents/biosynthesis , Biotechnology/methods , Cephamycins/biosynthesis , Culture Media , Mutation , Open Reading Frames/genetics , Streptomyces/genetics
6.
Mol Microbiol ; 70(5): 1180-93, 2008 Dec.
Article in English | MEDLINE | ID: mdl-18976279

ABSTRACT

Streptomyces coelicolor produces an extracellular protease inhibitor protein, STI (Streptomyces trypsin inhibitor). We show that post-growth elimination of STI is needed for colonies to develop aerial mycelium efficiently. Inactivation of STI, and thus the normal progression of colony development, at least partly involves an extracellular protease specified by gene SCO5913. Two-hybrid analysis identified two possible targets of STI inhibition (the products of SCO1355 and SCO5447), both extracellular proteases containing a domain homologous with the P-domain of eukaryotic convertases, proteases that mediate the processing of many precursors with important cellular or developmental roles. At least the SCO1355 protease is needed for the normal progression of development. Two components of the proposed cascade are dependent on the tRNA for the rare UUA (leucine) codon, which is specified by the developmental gene bldA. A model is presented that links intracellular regulatory events with an extracellular protease cascade to facilitate normal development.


Subject(s)
Bacterial Proteins/metabolism , Peptide Hydrolases/metabolism , Protease Inhibitors/metabolism , Streptomyces coelicolor/growth & development , Bacterial Proteins/genetics , DNA, Complementary/genetics , Fermentation , Gene Deletion , Gene Expression Regulation, Bacterial , Mutation , Protein Processing, Post-Translational , RNA, Bacterial/genetics , RNA, Transfer, Leu/metabolism , Streptomyces coelicolor/genetics , Streptomyces coelicolor/metabolism , Two-Hybrid System Techniques
7.
J Bacteriol ; 190(22): 7559-66, 2008 Nov.
Article in English | MEDLINE | ID: mdl-18790871

ABSTRACT

SCO4677 is one of a large number of similar genes in Streptomyces coelicolor that encode proteins with an HATPase_c domain resembling that of anti-sigma factors such as SpoIIAB of Bacillus subtilis. However, SCO4677 is not located close to genes likely to encode a cognate sigma or anti-anti-sigma factor. SCO4677 was found to regulate antibiotic production and morphological differentiation, both of which were significantly enhanced by the deletion of SCO4677. Through protein-protein interaction screening of candidate sigma factor partners using the yeast two-hybrid system, SCO4677 protein was found to interact with the developmentally specific sigma(F), suggesting that it is an antagonistic regulator of sigma(F). Two other proteins, encoded by SCO0781 and SCO0869, were found to interact with the SCO4677 anti-sigma(F) during a subsequent global yeast two-hybrid screen, and the SCO0869-SCO4677 protein-protein interaction was confirmed by coimmunoprecipitation. The SCO0781 and SCO0869 proteins resemble well-known anti-anti-sigma factors such as SpoIIAA of B. subtilis. It appears that streptomycetes may possess an extraordinary abundance of anti-sigma factors, some of which may influence diverse processes through interactions with multiple partners: a novel feature for such regulatory proteins.


Subject(s)
Bacterial Proteins/metabolism , Sigma Factor/metabolism , Streptomyces coelicolor/metabolism , Bacterial Proteins/genetics , Genetic Complementation Test , Immunoprecipitation , Mutation , Protein Binding , Sigma Factor/genetics , Streptomyces coelicolor/genetics , Two-Hybrid System Techniques
8.
J Microbiol Biotechnol ; 18(3): 417-26, 2008 Mar.
Article in English | MEDLINE | ID: mdl-18388457

ABSTRACT

The effect of increasing levels of proclavaminate amidino hydrolase (Pah) on the rate of clavulanic acid production in Streptomyces clavuligerus ATCC 27064 was evaluated by knock-in a gene (pah2) encoding Pah. A strain (SMF5703) harboring a multicopy plasmid containing the pah2 gene showed significantly retarded cell growth and reduced clavulanic acid production, possibly attributable to the deleterious effects of the multicopy plasmid. In contrast, a strain (SMF5704) carrying a single additional copy of pah2 introduced into chromosome via an integrative plasmid showed enhanced production of clavulanic acid and increased levels of pah2 transcripts. Analysis of transcripts of other genes involved in the clavulanic acid biosynthetic pathway revealed a pattern similar to that seen in the parent. From these results, it appears that clavulanic acid production can be enhanced by duplication of pah2 through integration of a second copy of the gene into chromosome. However, increasing the copy number of only one gene, such as pah2, does not affect the expression of other pathway genes, and so only modest improvements in clavulanic acid production can be expected. Flux controlled by Pah did increase when the copy number of pah2 was doubled, suggesting that under these growth conditions, Pah levels may be a limiting factor regulating the rate of clavulanic acid biosynthesis in S. clavuligerus.


Subject(s)
Clavulanic Acid/metabolism , Gene Expression , Streptomyces/enzymology , Ureohydrolases/genetics , Ureohydrolases/metabolism , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Biosynthetic Pathways , Fermentation , Gene Dosage , Gene Expression Regulation, Bacterial , Genetic Vectors , Kinetics , Streptomyces/genetics , Transcription, Genetic
9.
J Microbiol Biotechnol ; 18(12): 1884-9, 2008 Dec.
Article in English | MEDLINE | ID: mdl-19131688

ABSTRACT

The beta-lactamase inhibitory protein, BLIP-II, found in the culture supernatant of Streptomyces exfoliatus SMF19, shows no discernible sequence identity with other beta-lactamase inhibitory proteins identified in Streptomyces spp. A null mutant of the gene encoding BLIP-II (bliB::hygr) showed a bald appearance on solid media. Although BLIP-II was initially isolated from the supernatant of submerged cultures, sites of BLIP-II accumulation were seen in the cell envelope. The mutation of bliB was also associated with changes in the formation of septa and condensation of the chromosomal DNA associated with sporulation. The bliB mutant exhibited infrequent septa, showing dispersed chromosomal DNA throughout the mycelium, whereas the condensed chromosomes of the wild-type were separated by regularly spaced septa giving the appearance of a string of beads. Therefore, on the basis of these results, it is suggested that BLIP-II is a regulator of morphological differentiation in S. exfoliatus SMF19.


Subject(s)
Bacterial Proteins/metabolism , Streptomyces/cytology , Streptomyces/metabolism , beta-Lactamase Inhibitors , Bacterial Proteins/genetics , Cell Membrane/metabolism , Microscopy, Electron , Microscopy, Fluorescence , Mutation , Spores, Bacterial/physiology , Streptomyces/genetics , Streptomyces/ultrastructure , beta-Lactamases/genetics , beta-Lactamases/metabolism
10.
J Microbiol Biotechnol ; 17(2): 305-12, 2007 Feb.
Article in English | MEDLINE | ID: mdl-18051762

ABSTRACT

This study focused on the involvement of the unusual nucleotide (p)ppGpp, a stringent factor, during the morphological and physiological differentiation of Streptomyces coelicolor. Two genes, relA and rshA, were disrupted to demonstrate the roles of the stringent factor in the differentiation. The intracellular concentration of (p)ppGpp in the wild-type (M600) and disrupted mutants was measured in relation to the intentional starvation of a specific nutrient such as carbon, nitrogen, and phosphate or the in situ depletion of nutrients in a batch culture. As a result, it was found that the morphological characteristic of the deltarelA mutant was a bld phenotype forming condensed mycelia, whereas the deltarshA mutant grew fast-forming spores and straightforward mycelia. In both mutants, the production of actinorhodin (Act) was completely abolished, yet the undecylprodigiosin (Red) production was increased. Intracellular (p)ppGpp was detected in the deltarelA mutant in the case of limited phosphate, yet not with limited carbon or nitrogen sources. In contrast, (p)ppGpp was produced in the deltarshA mutant under limited carbon and nitrogen conditions. Therefore, (p)ppGpp in S. coelicolor was found to be selectively regulated by either the RelA or RshA protein, which was differentially expressed in response to the specific nutrient limitation. These results were also supported by the in situ ppGpp production during a batch culture. Furthermore, it is suggested that RelA and RshA are bifunctional proteins that possess the ability to both synthesize and hydrolyze (p)ppGpp.


Subject(s)
Bacterial Proteins/genetics , GTP Pyrophosphokinase/physiology , Ligases/genetics , Streptomyces coelicolor/metabolism , Anti-Bacterial Agents/biosynthesis , Bacterial Proteins/physiology , Ligases/physiology
11.
Appl Environ Microbiol ; 72(11): 7132-9, 2006 Nov.
Article in English | MEDLINE | ID: mdl-16950896

ABSTRACT

The objectives of the current studies were to determine the roles of key enzymes in central carbon metabolism in the context of increased production of antibiotics in Streptomyces coelicolor. Genes for glucose-6-phosphate dehydrogenase and phosphoglucomutase (Pgm) were deleted and those for the acetyl coenzyme A carboxylase (ACCase) were overexpressed. Under the conditions tested, glucose-6-phosphate dehydrogenase encoded by zwf2 plays a more important role than that encoded by zwf1 in determining the carbon flux to actinorhodin (Act), while the function of Pgm encoded by SCO7443 is not clearly understood. The pgm-deleted mutant unexpectedly produced abundant glycogen but was impaired in Act production, the exact reverse of what had been anticipated. Overexpression of the ACCase resulted in more rapid utilization of glucose and sharply increased the efficiency of its conversion to Act. From the current experiments, it is concluded that carbon storage metabolism plays a significant role in precursor supply for Act production and that manipulation of central carbohydrate metabolism can lead to an increased production of Act in S. coelicolor.


Subject(s)
Anti-Bacterial Agents/metabolism , Carbohydrate Metabolism/genetics , Genetic Engineering/methods , Streptomyces coelicolor/enzymology , Streptomyces coelicolor/genetics , Acetyl-CoA Carboxylase/genetics , Acetyl-CoA Carboxylase/metabolism , Anthraquinones/metabolism , Biotechnology/methods , Kinetics , Phosphoglucomutase/genetics , Phosphoglucomutase/metabolism , Streptomyces coelicolor/metabolism
12.
Mol Microbiol ; 60(4): 907-16, 2006 May.
Article in English | MEDLINE | ID: mdl-16677302

ABSTRACT

The emergence and dissemination of extended-spectrum (ES) beta-lactamases induce therapeutic failure and a lack of eradication of clinical isolates even by third-generation beta-lactam antibiotics like ceftazidime. CMY-10 is a plasmid-encoded class C beta-lactamase with a wide spectrum of substrates. Unlike the well-studied class C ES beta-lactamase from Enterobacter cloacae GC1, the Omega-loop does not affect the active site conformation and the catalytic activity of CMY-10. Instead, a three-amino-acid deletion in the R2-loop appears to be responsible for the ES activity of CMY-10. According to the crystal structure solved at 1.55 A resolution, the deletion significantly widens the R2 active site, which accommodates the R2 side-chains of beta-lactam antibiotics. This observation led us to demonstrate the hydrolysing activity of CMY-10 towards imipenem with a long R2 substituent. The forced mutational analyses of P99 beta-lactamase reveal that the introduction of deletion mutations into the R2-loop is able to extend the substrate spectrum of class C non-ES beta-lactamases, which is compatible with the isolation of natural class C ES enzymes harbouring deletion mutations in the R2-loop. Consequently, the opening of the R2 active site by the deletion of some residues in the R2-loop can be considered as an operative molecular strategy of class C beta-lactamases to extend their substrate spectrum.


Subject(s)
Enterobacter cloacae/enzymology , Plasmids/genetics , beta-Lactamases/chemistry , Amino Acid Sequence , Anti-Bacterial Agents/chemistry , Anti-Bacterial Agents/metabolism , Crystallography, X-Ray , Enterobacter cloacae/genetics , Hydrolysis , Imipenem/chemistry , Imipenem/metabolism , Molecular Sequence Data , Mutation , Protein Conformation , Sequence Deletion , Substrate Specificity , beta-Lactamases/genetics
13.
Microbiology (Reading) ; 151(Pt 8): 2707-2720, 2005 Aug.
Article in English | MEDLINE | ID: mdl-16079348

ABSTRACT

Previous proteomic analyses of Streptomyces coelicolor by two-dimensional electrophoresis and protein mass fingerprinting focused on extracts from total cellular material. Here, the membrane-associated proteome of cultures grown in a liquid minimal medium was partially characterized. The products of some 120 genes were characterized from the membrane fraction, with 70 predicted to possess at least one transmembrane helix. A notably high proportion of ABC transporter systems was represented; the specific types detected provided a snapshot of the nutritional requirements of the mycelium. The membrane-associated proteins did not change very much in abundance in different phases of growth in liquid minimal medium. Identification of gene products not expected to be present in membrane protein extracts led to a reconsideration of the genome annotation in two cases, and supplemented scarce information on 11 hypothetical/conserved hypothetical proteins of unknown function. The wild-type membrane proteome was compared with that of a bldA mutant lacking the only tRNA capable of efficient translation of the rare UUA (leucine) codon. Such mutants are unaffected in vegetative growth but are defective in many aspects of secondary metabolism and morphological differentiation. There were a few clear changes in the membrane proteome of the mutant. In particular, two hypothetical proteins (SCO4244 and SCO4252) were completely absent from the bldA mutant, and this was associated with the TTA-containing regulatory gene SCO4263. Evidence for the control of a cluster of function-unknown genes by the SCO4263 regulator revealed a new aspect of the pleiotropic bldA phenotype.


Subject(s)
DNA-Binding Proteins/genetics , Proteome/analysis , RNA, Bacterial/metabolism , RNA, Transfer, Leu/genetics , Streptomyces coelicolor/metabolism , Base Sequence , DNA, Bacterial/analysis , Gene Expression Regulation, Bacterial , Proteome/genetics , RNA, Bacterial/genetics , RNA, Transfer, Leu/metabolism , Streptomyces coelicolor/genetics , Streptomyces coelicolor/growth & development
14.
J Bacteriol ; 187(9): 2957-66, 2005 May.
Article in English | MEDLINE | ID: mdl-15838021

ABSTRACT

The extracellular proteome of Streptomyces coelicolor grown in a liquid medium was analyzed by using two-dimensional gel electrophoresis and matrix-assisted laser desorption ionization-time of flight peptide mass fingerprint analysis. Culture supernatants became protein rich only after rapid growth had been completed, supporting the idea that protein secretion is largely a stationary phase phenomenon. Out of about 600 protein spots observed, 72 were characterized. The products of 47 genes were identified, with only 11 examples predicted to be secreted proteins. Mutation in bldA, previously known to impair the stationary phase processes of antibiotic production and morphological differentiation, also induced changes in the extracellular proteome, revealing even greater pleiotropy in the bldA phenotype than previously known. Four proteins increased in abundance in the bldA mutant, while the products of 11 genes, including four secreted proteins, were severely down-regulated. Although bldA encodes the only tRNA capable of efficiently translating the rare UUA (leucine) codon, none of the latter group of genes contains an in-frame TTA. SCO0762, a serine-protease inhibitor belonging to the Streptomyces subtilisin inhibitor family implicated in differentiation in other streptomycetes, was completely absent from the bldA mutant. This dependence was shown to be mediated via the TTA-containing regulatory gene adpA, also known as bldH, a developmental gene that is responsible for the effects of bldA on differentiation. Mutation of the SCO0762 gene abolished detectable trypsin-protease inhibitory activity but did not result in any obvious morphological defects.


Subject(s)
DNA-Binding Proteins/genetics , Gene Expression Regulation, Bacterial , Proteome/genetics , RNA, Bacterial/genetics , RNA, Transfer/genetics , Streptomyces coelicolor/genetics , Trans-Activators/metabolism , Amino Acid Sequence , Bacterial Proteins/genetics , Bacterial Proteins/physiology , Base Sequence , DNA, Bacterial , Electrophoresis, Gel, Two-Dimensional , Gene Deletion , Molecular Sequence Data , Mutagenesis, Insertional , Proteome/analysis , Sequence Homology, Amino Acid , Serine Proteinase Inhibitors/genetics , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization , Streptomyces coelicolor/growth & development , Streptomyces coelicolor/metabolism , Trypsin/metabolism
15.
Nat Biotechnol ; 23(1): 63-8, 2005 Jan.
Article in English | MEDLINE | ID: mdl-15592456

ABSTRACT

We report the complete genome sequence of Zymomonas mobilis ZM4 (ATCC31821), an ethanologenic microorganism of interest for the production of fuel ethanol. The genome consists of 2,056,416 base pairs forming a circular chromosome with 1,998 open reading frames (ORFs) and three ribosomal RNA transcription units. The genome lacks recognizable genes for 6-phosphofructokinase, an essential enzyme in the Embden-Meyerhof-Parnas pathway, and for two enzymes in the tricarboxylic acid cycle, the 2-oxoglutarate dehydrogenase complex and malate dehydrogenase, so glucose can be metabolized only by the Entner-Doudoroff pathway. Whole genome microarrays were used for genomic comparisons with the Z. mobilis type strain ZM1 (ATCC10988) revealing that 54 ORFs predicted to encode for transport and secretory proteins, transcriptional regulators and oxidoreductase in the ZM4 strain were absent from ZM1. Most of these ORFs were also found to be actively transcribed in association with ethanol production by ZM4.


Subject(s)
Genome, Bacterial , Zymomonas/genetics , Biological Transport , DNA/chemistry , Ethanol/chemistry , Ethanol/metabolism , Genome , Ketoglutarate Dehydrogenase Complex/metabolism , Malate Dehydrogenase/metabolism , Models, Biological , Molecular Sequence Data , Multigene Family , Oligonucleotide Array Sequence Analysis , Open Reading Frames , Oxidative Stress , Plasmids/metabolism , RNA/chemistry , Sequence Analysis, DNA , Transcription, Genetic , Tricarboxylic Acids/metabolism
16.
J Biotechnol ; 114(1-2): 81-7, 2004 Oct 19.
Article in English | MEDLINE | ID: mdl-15464601

ABSTRACT

The effects of growth rate and nutrient uptake rate on the production of cephamycin C were determined in the parental strain, deltarelA mutant, and deltarsh null mutant of S. clavuligerus. Production of cephamycin C was inversely related to mycelium growth and the phosphate feed rate was more critical for the production of cephamycin C. On the contrary, the production of cephamycin C was completely abolished in the deltarelA mutant, but not in deltarsh mutant. The changes in the cephamycin C production by disruption of the relA and rsh genes are presumably associated with the consequent ability of the mutants to accumulate (p)ppGpp under nutrient starvation. Therefore, it is concluded that the stringent response of S. clavuligerus to starvation for nutrients is governed mainly by RelA rather than Rsh and that the response is more apparently regulated by the limitation of phosphate.


Subject(s)
Bacterial Proteins/metabolism , Cephamycins/biosynthesis , Glycerol/metabolism , Ligases/metabolism , Phosphates/metabolism , Streptomyces/genetics , Streptomyces/physiology , Anti-Bacterial Agents/biosynthesis , Bacterial Proteins/genetics , Cell Culture Techniques/methods , Cell Proliferation , Gene Expression Regulation, Bacterial/physiology , Ligases/genetics , Species Specificity
17.
Int J Antimicrob Agents ; 24(4): 320-6, 2004 Oct.
Article in English | MEDLINE | ID: mdl-15380255

ABSTRACT

Among the 51 clinical isolates collected from a university hospital in Korea, nine isolates were resistant to cephamycins. Nine isolates were shown to produce CMY-11 and these also included three isolates producing TEM-1. The results from ERIC-PCR revealed that dissemination of CMY-11 was due to outbreaks of resistant species and to the intra-species spread of resistance to cephamycins in Korea. CMY-11 beta-lactamase genes from nine clinical isolates that were responsible for resistance to cephamycins (cefoxitin and cefotetan), amoxicillin, cephalothin and amoxicillin-clavulanic acid, were cloned and characterised. A sequence identical to the common regions in In6, In7 and a novel integron from pSAL-1 was found upstream from bla(CMY-11) gene at nucleotide 1-71. Eighteen nucleotides between position 71 and 72 were inserted into the bla(CMY-11) gene.


Subject(s)
Bacterial Proteins/genetics , Escherichia coli/enzymology , beta-Lactamases/genetics , Bacterial Proteins/biosynthesis , Base Sequence , DNA Primers , DNA, Bacterial/genetics , Escherichia coli/classification , Escherichia coli/isolation & purification , Korea , Molecular Sequence Data , Polymerase Chain Reaction , beta-Lactamases/biosynthesis
18.
Microbiology (Reading) ; 150(Pt 5): 1485-1493, 2004 May.
Article in English | MEDLINE | ID: mdl-15133110

ABSTRACT

This study is focused on the involvement of the unusual nucleotide (p)ppGpp during the morphological and physiological differentiation of Streptomyces clavuligerus. In particular, the functional and structural elements of two genes encoding the proteins RelA and Rsh were identified. The relA gene encodes an 843 aa protein (RelA), while the rsh gene encodes a 738 aa protein (Rsh). The relA and rsh genes were disrupted by the insertion of a hygromycin resistance gene and an apramycin resistance gene, respectively. The synthesis of ppGpp in the relA gene-disrupted mutant was completely eliminated under conditions of starvation for amino acids, whereas synthesis persisted, but was greatly reduced in the rsh gene-disrupted mutant. The relA gene-disrupted mutant had a bald appearance on agar plate cultures and retarded growth in submerged culture, while the rsh-disrupted mutant was unchanged in growth characteristics relative to the wild-type culture. The production of both clavulanic acid and cephamycin C were completely abolished in the relA-disrupted mutant. Thus, it is concluded that the relA gene rather than rsh is essential for morphological and physiological differentiation in S. clavuligerus and that RelA primarily governs the stringent response of S. clavuligerus to starvation for amino acids.


Subject(s)
Bacterial Proteins/genetics , Gene Expression Regulation, Bacterial , Ligases/genetics , Streptomyces/growth & development , Streptomyces/physiology , Bacterial Proteins/metabolism , Cephamycins/biosynthesis , Clavulanic Acid/biosynthesis , Culture Media , Genetic Complementation Test , Guanosine Pentaphosphate/metabolism , Guanosine Tetraphosphate/metabolism , Ligases/metabolism , Molecular Sequence Data , Mutation , Phylogeny , Sequence Analysis, DNA , Streptomyces/genetics
19.
J Clin Microbiol ; 41(6): 2477-82, 2003 Jun.
Article in English | MEDLINE | ID: mdl-12791868

ABSTRACT

To determine the prevalence and genotype of an extended-spectrum beta-lactamase and new chromosomal AmpC beta-lactamases among clinical isolates of Enterobacter species, we performed antibiotic susceptibility testing, pI determination, induction tests, transconjugation, enterobacterial repetitive consensus (ERIC) PCR, sequencing, and phylogenetic analysis. Among the 51 clinical isolates collected from a university hospital in Korea, 6 isolates have been shown to produce SHV-12 and inducible AmpC beta-lactamases. These also included three isolates producing TEM-1b and one strain carrying TEM-1b and CMY-type beta-lactamases with a pI of 8.0. The results from ERIC PCR revealed that six isolates were genetically unrelated, suggesting that dissemination of SHV-12 was responsible for the spread of resistance to extended-spectrum beta-lactams in Korea. Six genes of inducible AmpC beta-lactamases that are responsible for the resistance to cephamycins (cefoxitin and cefotetan), amoxicillin, cephalothin, and amoxicillin-clavulanic acid were cloned and characterized. A 1,165-bp DNA fragment containing the ampC genes was sequenced and found to have an open reading frame coding for a 381-amino-acid beta-lactamase. The nucleotide sequence of four ampC genes (bla(EcloK992004.1), bla(EcloK995120.1), bla(EcloK99230), and bla(EareK9911729)) shared considerable homology with that of AmpC-type class C beta-lactamase genes of gram-negative bacteria, especially that of the chromosomal ampC gene (bla(EcloMHN1)) of Enterobacter cloacae MHN1 (99.9, 99.7, 99.6, and 99.6% identity, respectively). The sequences of two ampC genes (bla(EcloK9973) and bla(EcloK9914325)) showed close similarity to the chromosomal ampC gene (bla(EcloQ908R)) of E. cloacae Q908R (99.7% identity). The results from phylogenetic analysis suggested that six ampC genes could originate from bla(EcloMHN1) or bla(EcloQ908R).


Subject(s)
Bacterial Proteins , Enterobacter/enzymology , Enterobacteriaceae Infections/microbiology , beta-Lactamases/genetics , Conjugation, Genetic , Enterobacter/drug effects , Enterobacter/genetics , Humans , Isoelectric Focusing , Korea , Microbial Sensitivity Tests , Molecular Sequence Data , Phylogeny , Polymerase Chain Reaction , Repetitive Sequences, Nucleic Acid , Sequence Analysis, DNA , beta-Lactam Resistance , beta-Lactamases/chemistry , beta-Lactams/pharmacology
20.
J Antimicrob Chemother ; 49(2): 269-73, 2002 Feb.
Article in English | MEDLINE | ID: mdl-11815567

ABSTRACT

We report the description of a new plasmid-encoded AmpC-type beta-lactamase gene (bla(CMY-11)) from Escherichia coli K983802.1 that was isolated from a patient in South Korea suffering from a urinary tract infection. Antibiotic susceptibility testing, plasmid analysis, pI determination, transconjugation and Southern blot analysis were carried out to investigate the resistance mechanism to cefoxitin. PCR, sequencing and sequence analysis were used to identify and analyse the beta-lactamase gene (bla(CMY-11)) responsible for the cefoxitin resistance. CMY-11 and bla(CMY-11) are compared with other class C beta-lactamases and their genes to determine phylogenetic relationships. The cefoxitin-resistance phenotype of E. coli K983802.1 reflects the presence of a large plasmid [pYMG-2 (130 kb)]. A beta-lactamase with a pI value of 8.0 from a transconjugant of E. coli K983802.1 was identified by isoelectric focusing. A 1478 bp DNA fragment from pYMG-2 containing bla(CMY-11) was sequenced and an open reading frame coding for a 382 amino acid peptide (CMY-11) was found. Phylogenetic analysis clearly shows that bla(CMY-11) belongs to the group of ampC-related bla genes. It is likely that bla(CMY-11) evolved from bla(CMY-1) via bla(CMY-10).


Subject(s)
Bacterial Proteins , Escherichia coli/enzymology , Escherichia coli/genetics , Plasmids/genetics , beta-Lactamases/genetics , Amino Acid Sequence , Base Sequence/genetics , Cefoxitin/pharmacology , Drug Resistance, Bacterial/genetics , Escherichia coli/drug effects , Escherichia coli/isolation & purification , Escherichia coli Infections/enzymology , Escherichia coli Infections/microbiology , Female , Humans , Korea/epidemiology , Middle Aged , Molecular Sequence Data , Urinary Tract Infections/enzymology , Urinary Tract Infections/microbiology
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