Identification of the Biosynthetic Gene Cluster and an Additional Gene for Resistance to the Antituberculosis Drug Capreomycin

Capreomycin (CMN) belongs to the tuberactinomycin family of nonribosomal peptide antibiotics that are essential components of the drug arsenal for the treatment of multidrug-resistant tuberculosis. Members of this antibiotic family target the ribosomes of sensitive bacteria and disrupt the function of both subunits of the ribosome. Resistance to these antibiotics in Mycobacterium species arises due to mutations in the genes coding for the 16S or 23S rRNA but can also arise due to mutations in a gene coding for an rRNA-modifying enzyme, TlyA. While Mycobacterium species develop resistance due to alterations in the drug target, it has been proposed that the CMN-producing bacterium, Saccharothrix mutabilis subsp. capreolus, uses CMN modification as a mechanism for resistance rather than ribosome modification. To better understand CMN biosynthesis and resistance in S. mutabilis subsp. capreolus, we focused on the identification of the CMN biosynthetic gene cluster in this bacterium. Here, we describe the cloning and sequence analysis of the CMN biosynthetic gene cluster from S. mutabilis subsp. capreolus ATCC 23892. We provide evidence for the heterologous production of CMN in the genetically tractable bacterium Streptomyces lividans 1326. Finally, we present data supporting the existence of an additional CMN resistance gene. Initial work suggests that this resistance gene codes for an rRNA-modifying enzyme that results in the formation of CMN-resistant ribosomes that are also resistant to the aminoglycoside antibiotic kanamycin. Thus, S. mutabilis subsp. capreolus may also use ribosome modification as a mechanism for CMN resistance.     

Identification of an Iron-Sulfur Cluster That Modulates the Enzymatic Activity in NarE, a Neisseria meningitidis ADP-ribosyltransferase

In prokaryotes, mono-ADP-ribose transfer enzymes represent a family of exotoxins that display activity in a variety of bacterial pathogens responsible for causing disease in plants and animals, including those affecting mankind, such as diphtheria, cholera, and whooping cough. We report here that NarE, a putative ADP-ribosylating toxin previously identified from Neisseria meningitidis, which shares structural homologies with Escherichia coli heat labile enterotoxin and toxin from Vibrio cholerae, possesses an iron-sulfur center. The recombinant protein was expressed in E. coli, and when purified at high concentration, NarE is a distinctive golden brown in color. Evidence from UV-visible spectrophotometry and EPR spectroscopy revealed characteristics consistent of an iron-binding protein. The presence of iron was determined by colorimetric method and by an atomic absorption spectrophotometer. To identify the amino acids involved in binding iron, a combination of site-directed mutagenesis and UV-visible and enzymatic assays were performed. All four cysteine residues were individually replaced by serine. Substitution of Cys⁶⁷ and Cys¹²⁸ into serine caused a drastic reduction in the E₄₂₀/E₂₈₀ ratio, suggesting that these two residues are essential for the formation of a stable coordination. This modification led to a consistent loss in ADP-ribosyltransferase activity, while decrease in NAD-glycohydrolase activity was less dramatic in these mutants, indicating that the correct assembly of the iron-binding site is essential for transferase but not hydrolase activity. This is the first observation suggesting that a member of the ADP-ribosyltransferase family contains an Fe-S cluster implicated in catalysis. This observation may unravel novel functions exerted by this class of enzymes.     

Identification and Functional Analysis of Trypanosoma cruzi Genes That Encode Proteins of the Glycosylphosphatidylinositol Biosynthetic Pathway

Background

Trypanosoma cruzi is a protist parasite that causes Chagas disease. Several proteins that are essential for parasite virulence and involved in host immune responses are anchored to the membrane through glycosylphosphatidylinositol (GPI) molecules. In addition, T. cruzi GPI anchors have immunostimulatory activities, including the ability to stimulate the synthesis of cytokines by innate immune cells. Therefore, T. cruzi genes related to GPI anchor biosynthesis constitute potential new targets for the development of better therapies against Chagas disease.

Methodology/Principal Findings

In silico analysis of the T. cruzi genome resulted in the identification of 18 genes encoding proteins of the GPI biosynthetic pathway as well as the inositolphosphorylceramide (IPC) synthase gene. Expression of GFP fusions of some of these proteins in T. cruzi epimastigotes showed that they localize in the endoplasmic reticulum (ER). Expression analyses of two genes indicated that they are constitutively expressed in all stages of the parasite life cycle. T. cruzi genes TcDPM1, TcGPI10 and TcGPI12 complement conditional yeast mutants in GPI biosynthesis. Attempts to generate T. cruzi knockouts for three genes were unsuccessful, suggesting that GPI may be an essential component of the parasite. Regarding TcGPI8, which encodes the catalytic subunit of the transamidase complex, although we were able to generate single allele knockout mutants, attempts to disrupt both alleles failed, resulting instead in parasites that have undergone genomic recombination and maintained at least one active copy of the gene.

Conclusions/Significance

Analyses of T. cruzi sequences encoding components of the GPI biosynthetic pathway indicated that they are essential genes involved in key aspects of host-parasite interactions. Complementation assays of yeast mutants with these T. cruzi genes resulted in yeast cell lines that can now be employed in high throughput screenings of drugs against this parasite.     

来源卤化二型聚酮类生物合成基因簇的两种关键功能基因鉴定与表达

为催化卤化产物,挖掘具有生物活性的新卤化物提供新的方法途径,拟构建卤化酶原核表达载体催化天然卤化物的卤化过程.对链霉菌Streptomyces sp.FJS31-2基因组中一个II型PKS类产物zunyimycin生物合成基因簇进行系列分析,针对其中的后修饰酶卤化酶基因和单加氧酶基因进行原核表达纯化.通过分子生物学手段...     

天然产物5,6,7,3′,4′-五甲氧基异黄酮的合成(英文)

以3,4-二甲氧基苯乙酸和3,4,5-三甲氧基苯酚为原料,通过一条包括酯化反应、Fries重排、以及Vilsmeier-Haack反应等5步反应的路线合成了天然产物5,6,7,3′,4′-五甲氧基异黄酮。根据3,4,5-三甲氧基苯酚计算目标产物的总收率为76%,利用NMR及元素分析确证了化合物的结构。     

Identification and Analysis of the Biosynthetic Gene Cluster Encoding the Thiopeptide Antibiotic Cyclothiazomycin in Streptomyces hygroscopicus 10-22

Thiopeptide antibiotics are an important class of natural products resulting from posttranslational modifications of ribosomally synthesized peptides. Cyclothiazomycin is a typical thiopeptide antibiotic that has a unique bridged macrocyclic structure derived from an 18-amino-acid structural peptide. Here we reported cloning, sequencing, and heterologous expression of the cyclothiazomycin biosynthetic gene cluster from Streptomyces hygroscopicus 10-22. Remarkably, successful heterologous expression of a 22.7-kb gene cluster in Streptomyces lividans 1326 suggested that there is a minimum set of 15 open reading frames that includes all of the functional genes required for cyclothiazomycin production. Six genes of these genes, cltBCDEFG flanking the structural gene cltA, were predicted to encode the enzymes required for the main framework of cyclothiazomycin, and two enzymes encoded by a putative operon, cltMN, were hypothesized to participate in the tailoring step to generate the tertiary thioether, leading to the final cyclization of the bridged macrocyclic structure. This rigorous bioinformatics analysis based on heterologous expression of cyclothiazomycin resulted in an ideal biosynthetic model for us to understand the biosynthesis of thiopeptides.The thiopeptides are a family of highly modified, sulfur-containing macrocyclic peptides, such as thiostrepton, thiocillins, and micrococcinic acid (3, 11). Their structures have several common features: a tri- or tetrasubstituted nitrogen heterocycle central domain, a macrocyclic framework, and heavily modified amino acid residues, including thiazoles, oxazoles, and dehydroamino acids (Fig. ​(Fig.1)1) (3). Members of this family exhibit various biological properties, such as inhibition of ribosomal protein synthesis (24), rennin inhibitory activity (2), and induction of TipA (20). Moreover, many thiopeptide antibiotics show bioactivity against some bacterial strains resistant to most conventional treatments, including methicillin-resistant Staphylococcus aureus (MRSA), penicillin-resistant Streptococcus pneumoniae (PRSP), and vancomycin-resistant enterococci (VRE) (3, 17).Open in a separate windowFIG. 1.Structures of thiostrepton, thiocillin, microncoccinate, and cyclothiazomycin (3).Early in vitro investigations of these special heterocycles of thiopeptides were performed by organic chemists and included stereoselective synthesis of a γ-lactam acidic hydrolysate of cyclothiazomycin (4) and total synthesis of thiostrepton (21). Extensive research on microccins (5, 19) and lantibiotics (6, 29) described biosynthesis of the thiazole- and dehydroamino acid-containing polypeptides that were derived from ribosomally synthesized prepeptides. Similarly, Lee et al. described a widely conserved gene cluster for toxin biosynthesis and suggested a ribosome biosynthetic pathway for the modified polypeptide containing thiazoles and oxazoles (16).Recently, Wieland Brown et al. (28) and Kelly et al. (14) identified the gene clusters encoding thiocillin and thiostrepton, respectively, with a probe that targeted hypothetic prepeptide genes, whereas Liao and coworkers (17) took advantage of the conservation of one putative cyclodehydratase. Although most of the biochemical reactions involved in the biosynthetic pathway remain obscure, it is clear that thiopeptides are synthesized ribosomally and then there is a series of posttranslational modifications.Cyclothiazomycin, which was isolated as a novel selective inhibitor of human plasma rennin, is a unique bridged macrocyclic thiopeptide (2) whose stereo structure was recently revealed by degradation experiments and spectroscopic analysis (10). It contains a dehydroserine, two dehydrothreonine residues, three thiazolines, three thiazoles, and a trisubstituted pyridine. Compared with common thiopeptides, it lacks the characteristic 2- and 3-azole substituent on the central pyridine domain; instead, it has an alanine-derived heterocyclic residue with the (R) configuration, a quaternary sulfide, and two macrocyclic peptide loops (Fig. ​(Fig.1).1). Moreover, a pair of convertible isomers of cyclothiazomycin B, the cyclothiazomycin analogues produced by Streptomyces sp. strain A307 (10), were identified as Z and E configurations caused by the tautomerization of the dehydrated threonine. These structural traits may indicate that some new genetic elements are likely involved in posttranslational modification.Here we reported cloning and sequencing of the cyclothiazomycin biosynthetic gene cluster of Streptomyces hygroscopicus 10-22 (23). In addition, an analysis of heterologous expression in Streptomyces lividans 1326 and a deletion analysis were also performed, which indicated that a gene cluster at least 22.7 kb long is required for biosynthesis. A bioinformatics-based approach to analysis of this gene cluster postulated that there is a posttranslational modification pathway in which eight proteins are involved in the biosynthetic machinery.     

Identification of the Biosynthetic Gene Cluster for the Pseudomonas aeruginosa Antimetabolite l-2-Amino-4-Methoxy-trans-3-Butenoic Acid

l-2-Amino-4-methoxy-trans-3-butenoic acid (AMB) is a potent antibiotic and toxin produced by Pseudomonas aeruginosa. Using a novel biochemical assay combined with site-directed mutagenesis in strain PAO1, we have identified a five-gene cluster specifying AMB biosynthesis, probably involving a thiotemplate mechanism. Overexpression of this cluster in strain PA7, a natural AMB-negative isolate, led to AMB overproduction.The Gram-negative bacterium Pseudomonas aeruginosa is an opportunistic pathogen that causes a wide range of human infections and is considered the main pathogen responsible for chronic pneumonia in cystic fibrosis patients (7, 23). P. aeruginosa also infects other organisms, such as insects (4), nematodes (6), plants (18), and amoebae (20). Its ability to thrive as a pathogen and to compete in aquatic and soil environments can be partly attributed to the production and interplay of secreted virulence factors and secondary metabolites. While the importance of many of these exoproducts has been studied, the antimetabolite l-2-amino-4-methoxy-trans-3-butenoic acid (AMB; methoxyvinylglycine) (Fig. ​(Fig.1)1) has received only limited attention. Identified during a search for new antibiotics, AMB was found to reversibly inhibit the growth of Bacillus spp. (26) and Escherichia coli (25) and was later shown to inhibit the growth and metabolism of cultured Walker carcinosarcoma cells (28). AMB is a γ-substituted vinylglycine, a naturally occurring amino acid with a β,γ-C=C double bond. Other members of this family are aminoethoxyvinylglycine from Streptomyces spp. (19) and rhizobitoxine, made by Bradyrhizobium japonicum (16) and Pseudomonas andropogonis (15) (Fig. ​(Fig.1).1). As inhibitors of pyridoxal phosphate-dependent enzymes (13, 17, 21, 22), γ-substituted vinylglycines have multiple targets in bacteria, animals, and plants (3, 5, 10, 21, 22, 29). However, the importance of AMB as a toxin in biological interactions with P. aeruginosa has not been addressed, as AMB biosynthesis and the genes involved have not been elucidated.Open in a separate windowFIG. 1.Chemical structures of the γ-substituted vinylglycines AMB, aminoethoxyvinylglycine, and rhizobitoxine.     

Identification of the Biosynthetic Gene Cluster for 3-Methylarginine,a Toxin Produced by Pseudomonas syringae pv. syringae 22d/93

The epiphyte Pseudomonas syringae pv. syringae 22d/93 (Pss22d) produces the rare amino acid 3-methylarginine (MeArg), which is highly active against the closely related soybean pathogen Pseudomonas syringae pv. glycinea. Since these pathogens compete for the same habitat, Pss22d is a promising candidate for biocontrol of P. syringae pv. glycinea. The MeArg biosynthesis gene cluster codes for the S-adenosylmethionine (SAM)-dependent methyltransferase MrsA, the putative aminotransferase MrsB, and the amino acid exporter MrsC. Transfer of the whole gene cluster into Escherichia coli resulted in heterologous production of MeArg. The methyltransferase MrsA was overexpressed in E. coli as a His-tagged protein and functionally characterized (K_m, 7 mM; k_cat, 85 min⁻¹). The highly selective methyltransferase MrsA transfers the methyl group from SAM into 5-guanidino-2-oxo-pentanoic acid to yield 5-guanidino-3-methyl-2-oxo-pentanoic acid, which then only needs to be transaminated to result in the antibiotic MeArg.Microbial plant pathogens cause severe losses in agriculture each year (1). For example, the plant pathogen Pseudomonas syringae pv. glycinea is responsible for bacterial blight of soybean, a leaf spot disease of great economic impact. Besides chemical treatment, biocontrol agents that antagonize microbial plant pathogens are gaining increasing importance in fighting plant diseases (6, 11, 27). In a screening for possible biocontrol strains, an epiphytic bacterium showing a strong and selective activity against the pathogen P. syringae pv. glycinea was isolated from soybean leaves (29). The strain was characterized as Pseudomonas syringae pv. syringae 22d/93 (Pss22d). The antagonism of Pss22d against P. syringae pv. glycinea has been demonstrated successfully in vitro and in planta under greenhouse and field conditions (19, 29). In order to identify the molecular basis of the antagonism of Pss22d against P. syringae pv. glycinea, we focused on its secondary metabolites. Besides the well-known lipodepsipeptides syringomycin and syringopeptin (3), Pss22d produces the rare amino acid 3-methylarginine (MeArg) (5). As little as 20 nmol of MeArg strongly and selectively inhibits P. syringae pv. glycinea but no other pseudomonads in vitro (29). Since the inhibition can be compensated for by l-arginine supplementation but not by any other essential amino acid, it is likely that the toxin acts as an inhibitor of the arginine biosynthesis pathway or an arginine-dependent pathway, such as nitric oxide formation (13, 16). Feeding experiments and Tn5 transposon mutagenesis suggested that MeArg is produced by an S-adenosyl methionine (SAM)-dependent methyltransferase (5) converting the enol of 5-guanidino-2-oxo-pentanoic acid to 5-guanidino-3-methyl-2-oxo-pentanoic acid. An analogous reaction is known to occur with the methyltransferases GlmT, DptI, and LptI, which form 3-methylglutamate from α-ketoglutarate (18). On the way to MeArg, only a transaminase catalyzing the formation of MeArg from 5-guanidino-3-methyl-2-oxo-pentanoic acid and an amino acid exporter to secrete the toxin would be needed.Here, we describe the identification and functional characterization of the MeArg biosynthesis gene cluster from the epiphyte Pss22d.     

Enteric YaiW Is a Surface-Exposed Outer Membrane Lipoprotein That Affects Sensitivity to an Antimicrobial Peptide

yaiW is a previously uncharacterized gene found in enteric bacteria that is of particular interest because it is located adjacent to the sbmA gene, whose bacA ortholog is required for Sinorhizobium meliloti symbiosis and Brucella abortus pathogenesis. We show that yaiW is cotranscribed with sbmA in Escherichia coli and Salmonella enterica serovar Typhi and Typhimurium strains. We present evidence that the YaiW is a palmitate-modified surface exposed outer membrane lipoprotein. Since BacA function affects the very-long-chain fatty acid (VLCFA) modification of S. meliloti and B. abortus lipid A, we tested whether SbmA function might affect either the fatty acid modification of the YaiW lipoprotein or the fatty acid modification of enteric lipid A but found that it did not. Interestingly, we did observe that E. coli SbmA suppresses deficiencies in the VLCFA modification of the lipopolysaccharide of an S. meliloti bacA mutant despite the absence of VLCFA in E. coli. Finally, we found that both YaiW and SbmA positively affect the uptake of proline-rich Bac7 peptides, suggesting a possible connection between their cellular functions.     

Identification of an Imprinted Gene Cluster in the X-Inactivation Center

Mammalian development is strongly influenced by the epigenetic phenomenon called genomic imprinting, in which either the paternal or the maternal allele of imprinted genes is expressed. Paternally expressed Xist, an imprinted gene, has been considered as a single cis-acting factor to inactivate the paternally inherited X chromosome (Xp) in preimplantation mouse embryos. This means that X-chromosome inactivation also entails gene imprinting at a very early developmental stage. However, the precise mechanism of imprinted X-chromosome inactivation remains unknown and there is little information about imprinted genes on X chromosomes. In this study, we examined whether there are other imprinted genes than Xist expressed from the inactive paternal X chromosome and expressed in female embryos at the preimplantation stage. We focused on small RNAs and compared their expression patterns between sexes by tagging the female X chromosome with green fluorescent protein. As a result, we identified two micro (mi)RNAs–miR-374-5p and miR-421-3p–mapped adjacent to Xist that were predominantly expressed in female blastocysts. Allelic expression analysis revealed that these miRNAs were indeed imprinted and expressed from the Xp. Further analysis of the imprinting status of adjacent locus led to the discovery of a large cluster of imprinted genes expressed from the Xp: Jpx, Ftx and Zcchc13. To our knowledge, this is the first identified cluster of imprinted genes in the cis-acting regulatory region termed the X-inactivation center. This finding may help in understanding the molecular mechanisms regulating imprinted X-chromosome inactivation during early mammalian development.     

Cloning and Heterologous Expression of the Vibrioferrin Biosynthetic Gene Cluster from a Marine Metagenomic Library

A biosynthetic gene cluster of siderophore consisting of five open reading frames (ORFs) was cloned by functional screening of a metagenomic library constructed from tidal-flat sediment. Expression of the cloned biosynthetic genes in Escherichia coli led to the production of vibrioferrin, a siderophore originally reported for the marine bacterium Vibrio parahaemolyticus. To the best of our knowledge, this is the first example of heterologous production of a siderophore by biosynthetic genes cloned from a metagenomic library. The cloned cluster was one of the largest of the clusters obtained by functional screening. In this study, we demonstrated and extended the possibility of function-based metagenomic research.     

Isolation and Characterization of the Gibberellin Biosynthetic Gene Cluster in Sphaceloma manihoticola

Gibberellins (GAs) are tetracyclic diterpenoid phytohormones that were first identified as secondary metabolites of the fungus Fusarium fujikuroi (teleomorph, Gibberella fujikuroi). GAs were also found in the cassava pathogen Sphaceloma manihoticola, but the spectrum of GAs differed from that in F. fujikuroi. In contrast to F. fujikuroi, the GA biosynthetic pathway has not been studied in detail in S. manihoticola, and none of the GA biosynthetic genes have been cloned from the species. Here, we present the identification of the GA biosynthetic gene cluster from S. manihoticola consisting of five genes encoding a bifunctional ent-copalyl/ent-kaurene synthase (CPS/KS), a pathway-specific geranylgeranyl diphosphate synthase (GGS2), and three cytochrome P450 monooxygenases. The functions of all of the genes were analyzed either by a gene replacement approach or by complementing the corresponding F. fujikuroi mutants. The cluster organization and gene functions are similar to those in F. fujikuroi. However, the two border genes in the Fusarium cluster encoding the GA₄ desaturase (DES) and the 13-hydroxylase (P450-3) are absent in the S. manihoticola GA gene cluster, consistent with the spectrum of GAs produced by this fungus. The close similarity between the two GA gene clusters, the identical gene functions, and the conserved intron positions suggest a common evolutionary origin despite the distant relatedness of the two fungi.     

Synthesis of the Natural Product 5'-Deoxy-5-iodotubercidin and Related Halogenated Analogs

Abstract

5'-Deoxy-5-iodotubercidin, a novel nucleoside recently isolated from a marine source, has been synthesized in four steps from tubercidin. The intermediate 5'-deoxytubercidin was also used to prepare the 5-bromo and 5-chloro derivatives, as well as a series of 5, 6-dihalo compounds.     

Identification of a CArG Box-Dependent Enhancer within the Cysteine-Rich Protein 1 Gene That Directs Expression in Arterial but Not Venous or Visceral Smooth Muscle Cells

Smooth muscle cells (SMCs) are heterogeneous with respect to their contractile, synthetic, and proliferative properties, though the regulatory factors responsible for their phenotypic diversity remain largely unknown. To further our understanding of smooth muscle gene regulation, we characterized the cis-regulatory elements of the murine cysteine-rich protein 1 gene (CRP1/Csrp1). CRP1 is expressed in all muscle cell types during embryogenesis and predominates in vascular and visceral SMCs in the adult. We identified a 5-kb enhancer within the CRP1 gene that is sufficient to drive expression in arterial but not venous or visceral SMCs in transgenic mice. This enhancer also exhibits region-specific activity in the outflow tract of the heart and the somites. Within the 5-kb CRP1 enhancer, we found a single CArG box that binds serum response factor (SRF), and by mutational analysis, demonstrate that the activity of the enhancer is dependent on this CArG element. Our findings provide further evidence for the existence of distinct regulatory programs within SMCs and suggest a role for SRF in the activation of the CRP1 gene.