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Manipulation of Carrier Proteins in Antibiotic Biosynthesis
Abstract
Engineering biosynthetic pathways into suitable host organisms has become an attractive venue for the design, evaluation, and production of small molecule therapeutics. Polyketide (PK) and nonribosomal peptide (NRP) synthases have been of particular interest due to their modular structure, yet routine cloning and expression of these enzymes remains challenging. Here we describe a method to covalently label carrier proteins from PK and NRP synthases using the enzymatic transfer of a modified coenzyme A analog by a 4'-phosphopantetheinyltransferase. Using this method, carrier proteins can be loaded with single fluorescent or affinity reporters, providing novel entry for protein visualization, Western blot identification, and affinity purification. Application of these methods provides an ideal tool to track and quantify metabolically engineered pathways. Such techniques are valuable to measure protein expression, solubility, activity, and native posttranslational modification events in heterologous systems.
... P. aeruginosa AcpH was shown to remove coumarin-or rhodamine-modified Ppt from different CPs (17). Our biotinylated probe is reminiscent of maleimide (MAL)linked biotin-CoA conjugated probes (11,18), but we replaced the MAL linker with an acetamide (ACM) linker. The biotin-polyethylene glycol (PEG)-ACM-CoA probe (*CoA) avoided a problem encountered with the probe with a MAL linker, where reaction with CPs without addition of PPTase occurred upon denaturation of the samples for SDS-PAGE (not shown). ...
... To test the activity of PptH on native substrates, we developed a biotin-linked probe (biotin-PEG-ACM-CoA) for an assay to visualize the release of Ppt from CPs. This probe is reminiscent of those developed previously (11,18) but afforded lower background in our assays. We used the broad-specificity Sfp PPTase to covalently attach the probe to the conserved serine of CPs (18). ...
Phosphopantetheinyl hydrolase, PptH (Rv2795c), is a recently discovered enzyme from Mycobacterium tuberculosis that removes 4′-phosphopantetheine (Ppt) from holo-carrier proteins (CPs) and thereby opposes the action of phosphopantetheinyl transferases (PPTases). PptH is the first structurally characterized enzyme of the phosphopantetheinyl hydrolase family. However, conditions for optimal activity of PptH have not been defined, and only one substrate has been identified. Here, we provide biochemical characterization of PptH and demonstrate that the enzyme hydrolyzes Ppt in vitro from more than one M. tuberculosis holo-CP as well as holo-CPs from other organisms. PptH provided the only detectable activity in mycobacterial lysates that dephosphopantetheinylated acyl carrier protein M (AcpM), suggesting that PptH is the main Ppt hydrolase in M. tuberculosis. We could not detect a role for PptH in coenzyme A (CoA) salvage, and PptH was not required for virulence of M. tuberculosis during infection of mice. It remains to be determined why mycobacteria conserve a broadly acting phosphohydrolase that removes the Ppt prosthetic group from essential CPs. We speculate that the enzyme is critical for aspects of the life cycle of M. tuberculosis that are not routinely modeled.
IMPORTANCE Tuberculosis (TB), caused by Mycobacterium tuberculosis, was the leading cause of death from an infectious disease before COVID, yet the in vivo essentiality and function of many of the protein-encoding genes expressed by M. tuberculosis are not known. We biochemically characterize M. tuberculosis’s phosphopantetheinyl hydrolase, PptH, a protein unique to mycobacteria that removes an essential posttranslational modification on proteins involved in synthesis of lipids important for the bacterium’s cell wall and virulence. We demonstrate that the enzyme has broad substrate specificity, but it does not appear to have a role in coenzyme A (CoA) salvage or virulence in a mouse model of TB.
... Targeted modifications in the cellular machinery involved in posttranslational modifications can be used for the selective and fast imaging of cellular processes ex-vivo and in-vivo, drug or inhibitor delivery, or purification. However, their applications are limited to cell permeability of the cofactor analogues, and to the size and structure of the 30 modified enzymes that might prevent interaction between the structure of the substrate and the enzyme (Foley and Burkart, 2007;La Clair et al., 2004;Zhou et al., 2007) . ...
... As PCP and ACP are domains that can be present as single units or as part of the domains in a protein, this technology has been exploited to label a wide range of proteins with biotin or fluorophores (Rashidian et al., 2013). La Clair et al. (2004) engineered an analogous CoA to react with a maleimide-linked fluorescent reporter (Scheme 1-6). Fluorescent analogues of the natural cofactor for PPTases have been successfully used and fusion of carrier proteins (CP) proteins with other proteins are functional for labelling too (George et al., 2004). ...
Development of enzymatic labelling methods has been driven by the importance of studying molecular structures and interactions to comprehend cellular processes. Methyltransferases (MTases), which regulate genetic expression by transferring a methyl group from the cofactor S-adenosyl-L-methionine (SAM) to DNA, histones and various proteins, have been shown to accept SAM analogues with an alternative alkyl group on the sulfonium centre. These alkyl groups can be transferred to the substrate, and with a further reaction can be selectively functionalized. Thus, MTases together with SAM analogues have emerged as novel labelling tools.
The project aims to use MTases to obtain an orthogonal system that can selectively use a SAM cofactor analogue to transfer functional chains to proteins with a specific motif. To achieve selectivity of the system, the SAM analogue cofactor was modified on the ribose ring; to obtain a new transferase activity of the system, the transferable methyl on the sulfonium centre was changed to a different substituent. SAM analogues were produced enzymatically with hMAT2A by using 3’-deoxy-ATP and methionine or ethionine. Mutants of SET8 and novel substrates were designed to have modifications at residues in the active site, within the vicinity of the ribose ring of SAM, and were assessed for selective activity with the new analogue cofactor. The results showed that the new cofactor 3’-deoxy-S-adenosyl-L-methionine (3’dSAM) was efficient in the mono-methylation of the substrate peptide RFRKVL, and that the mutant SET8 C270V exhibited over 13 fold MTase activity in presence of 3’dSAM and the RFRKVL substrate, in comparison with the activity with the WT sequence RHRKVL and the SAM cofactor.
In addition, glutathione S-transferase (GST) was used as a model protein to express the motif RFRKVL, to transform it into a potential substrate for SET8. Assessment of the MTase activity of SET8, 3’dSAM and the novel GST substrate indicated mono-methylation of the substrate. Moreover, the motif showed no interference with GST native activity.
Based on the observations, a new enzymatic system shows higher selectivity with a new analogue cofactor over SAM to effectively methylate proteins expressing the consensus RFRKVL.
... Leveraging prior experience, we prepared uorescently labeled probes (blue hexagon, Fig. 2b) for imaging specic ketosynthase enzymes, and crosslinking probes (black hexagon, Fig. 2b) for evaluation of the interaction between the ACPs and their partner ketosynthases. [28][29][30][31] The uorescent probes evaluated the domain reactivity and the crosslinkers probed protein$protein interactions. To further test the domain reactivity, we chose both a short C2 chain (a, n = 1, Fig. 2b) and a longer C6 chain (b, n = 3, Fig. 2b) for the uorescent probes (ESI Fig. S1 †). ...
Protein-reactive natural products such as the fungal metabolite cerulenin are recognized for their value as therapeutic candidates, due to their ability to selectively react with catalytic residues within a protein active site or a complex of protein domains. Here, we explore the development of fatty-acid and polyketide-synthase probes by synthetically modulating cerulenin's functional moieties. Using a mechanism-based approach, we reveal unique reactivity within cerulenin and adapt it for fluorescent labeling and crosslinking of fatty-acid and iterative type-I polyketide synthases. We also describe two new classes of silylcyanohydrin and silylhemiaminal masked crosslinking probes that serve as new tools for activity and structure studies of these biosynthetic pathways.
... The fluorescence polarization assay in the present study was based on the documented methods and further optimized the conditions for the better drug screening [12]. 4'PPT subunit of coenzyme A (CoA) was labelled with the fluorescent dye BODIPY TMR maleimide (Life Technologies, MA, USA) as described in the previous document to monitor the transfer of the phosphopantetheine group from CoA to Acp1 [29]. The initial components were 2-8 ng/μL Ppt2, 30 ng/μL Acp1 and 1:25 CoA-BTMR with assay buffer comprising 62.5 mM TRIS-HCl and 12.5 mM MgCl 2 (pH 6.75) [12]. ...
With the high-frequency use or abuse of antifungal drugs, the crisis of drug-resistant fungi continues to increase worldwide; in particular, the infection of drug-resistant Candida albicans brings the great challenge to the clinical treatment. Therefore, to decelerate the spread of this resistance, it is extremely urgent to facilitate the new antifungal targets with novel drugs. Phosphopantetheinyl transferases PPTases (Ppt2 in Candida albicans) had been identified in bacterium and fungi and mammals, effects as a vital enzyme in the metabolism of organisms in C. albicans. Ppt2 transfers the phosphopantetheinyl group of coenzyme A to the acyl carrier protein Acp1 in mitochondria for the synthesis of lipoic acid that is essential for fungal respiration, so making Ppt2 an ideal target for antifungal drugs. In this study, 110 FDA-approved drugs were utilized to investigate the Ppt2 inhibition against drug-resistant Candida albicans by the improved fluorescence polarization experiments, which have enough druggability and structural variety under the novel strategy of drug repurposing. Thereinto, eight agents revealed the favourable Ppt2 inhibitory activities. Further, broth microdilution assay of incubating C. albicans with these eight drugs showed that pterostilbene, procyanidine, dichlorophen and tea polyphenol had the superior MIC values. In summary, these findings provide more valuable insight into the treatment of drug-resistant C. albicans.
... TAMRA-CoA (4). Compound 4 was synthesized in situ using CoA biosynthetic enzymes (CoaA, CoaD, CoaE) as previously reported [14,15]. The 1 mL reaction volume was incubated at 37 • C shaking for 8-12 hours and contained 5 mM of TAMRA-C6-Pantethenamide (3), 32 mM ATP pH 8, 0.01 µg µL −1 S. aureus 6-His CoaA, 0.01 µg µL −1 E. coli MBP CoaD, and 0.01 µg µL −1 E. coli MBP-CoaE in 50 mM Tris/HCl buffer pH 7.5. ...
... To determine Sfp expression and functional activity in S. elongatus, we employed an assay for the addition of the fluorescently labeled pantetheine analogue (TAMRA-CoA) to the type II E. coli fatty acid synthase ACP (AcpP) (La Clair et al., 2004). Soluble protein extract from each recombinant cyanobacterium containing the heterologous Sfp enzyme or from S. elongatus wild-type strain AMC2302 was added to recombinant apo-AcpP in the presence of TAMRA-CoA. ...
The development of new heterologous hosts for polyketides production represents an excellent opportunity to expand the genomic, physiological, and biochemical backgrounds that better fit the sustainable production of these valuable molecules. Cyanobacteria are particularly attractive for the production of natural compounds because they have minimal nutritional demands and several strains have well established genetic tools. Using the model strain Synechococcus elongatus, a generic platform was developed for the heterologous production of polyketide synthase (PKS)-derived compounds. The versatility of this system is based on interchangeable modules harboring promiscuous enzymes for PKS activation and the production of PKS extender units, as well as inducible circuits for a regulated expression of the PKS biosynthetic gene cluster. To assess the capability of this platform, we expressed the mycobacterial PKS-based mycocerosic biosynthetic pathway to produce multimethyl-branched esters (MBE). This work is a foundational step forward for the production of high value polyketides in a photosynthetic microorganism.
... transglutaminases and peptidases) and oxidoreductases (e.g. tyrosinases and peroxidases), are few systems employed for such immobilizations [136][137][138][139]. Recently, Sortase A (Srt A)-mediated ligation strategy has been established [140,141]. ...
Immobilized antibody systems are the key to develop efficient diagnostics and separations tools. In the last decade, developments in the field of biomolecular engineering and crosslinker chemistry have greatly influenced the development of this field. With all these new approaches at our disposal, several new immobilization methods have been created to address the main challenges associated with immobilized antibodies. Few of these challenges that we have discussed in this review are mainly associated to the site-specific immobilization, appropriate orientation, and activity retention. We have discussed the effect of antibody immobilization approaches on the parameters on the performance of an immunoassay.
... The coenzyme A analogue Bodipy-CoA was prepared as previously described. 38 To label thiolation domains of GrsA and GrsB1, standard CFPS reactions with 26.7 μg/mL of each plasmid were incubated at 30°C for 17 h. Afterward, labeling reactions were performed following three strategies. ...
Genome sequencing has revealed that a far greater number of natural product biosynthetic pathways exist than there are known natural products. To access these molecules directly and deterministically, a new generation of heterologous expression methods is needed. Cell-free protein synthesis has not previously been used to study nonribosomal peptide biosynthesis, and provides a tunable platform with advantages over conventional methods for protein expression. Here, we demonstrate the use of cell-free protein synthesis to biosynthesize a cyclic dipeptide with correct absolute stereochemistry. From a single-pot reaction, we measured the expression of two nonribosomal peptide synthetases larger than 100 kDa, and detected high-level production of a diketopiperazine. Using quantitative LC-MS and synthetically prepared standard, we observed production of this metabolite at levels higher than previously reported from cell-based recombinant expression, approximately 12 mg/L. Overall, this work represents a first step to apply cell-free protein synthesis to discover and characterize new natural products.
... NIH/3T3 cell line was purchased from Beijing Xiehe Cell Resource Center. Triton X-100 was purchased from Aladdin Chemistry Co. Ltd. 4 ...
Nano-biointerfaces with varied surface charge can be readily fabricated by integrating a template-based process with maleimide-thiol coupling chemistry. Significantly, nanostructures are employed for amplifying the effect of surface charge on cell adhesion, as revealed by the cell-adhesion performance, cell morphology and corresponding cytoskeletal organization. This study may provide a promising strategy for developing new biomedical materials with tailored cell adhesion for tissue implantation and regeneration.
... [28]. Moreover, due to its low substrate specificity it accepts various CoA analogs including covalently attached reporter molecules like affinity or fluorescent tags and thus can be used as a biochemical toolbox or to label specific protein tags [29,30]. ...
In the last decades, natural products from lichens have gained more interest for pharmaceutical application due to the broad range of their biological activity. However, isolation of the compounds of interest directly from the lichen is neither feasible nor sustainable due to slow growth of many lichens. In order to develop a pipeline for heterologous expression of lichen biosynthesis gene clusters and thus the sustainable production of their bioactive compounds we have identified and characterized the phosphopantheteinyl transferase (PPTase) EppA from the lichen Evernia prunastri. The Sfp-type PPTase EppA was functionally characterized through heterologous expression in E. coli using the production of the blue pigment indigoidine as readout and by complementation of a lys5 deletion in S. cerevisiae.
... In order to monitor the transfer of a phosphopantetheine group from coenzyme A to a target protein, a fluorescent dye BODIPY TMR maleimide (Life Technologies) was attached to the terminal sulphydryl group of coenzyme A [21]. CoA was labelled with BODIPY TMR maleimide as described previously [10]. ...
Antifungal drugs acting via new mechanisms of action are urgently needed to combat the increasing numbers of severe fungal infections caused by pathogens such as Candida albicans. The phosphopantetheinyl transferase of Aspergillus fumigatus, encoded by the essential gene pptB, has previously been identified as a potential antifungal target. This study investigated the function of its orthologue in C. albicans, PPT2/C1_09480W by placing one allele under the control of the regulatable MET3 promoter, and deleting the remaining allele. The phenotypes of this conditional null mutant showed that, as in A. fumigatus, the gene PPT2 is essential for growth in C. albicans, thus fulfilling one aspect of an efficient antifungal target. The catalytic activity of Ppt2 as a phosphopantetheinyl transferase and the acyl carrier protein Acp1 as a substrate were demonstrated in a fluorescence transfer assay, using recombinant Ppt2 and Acp1 produced and purified from E.coli. A fluorescence polarisation assay amenable to high-throughput screening was also developed. Therefore we have identified Ppt2 as a broad-spectrum novel antifungal target and developed tools to identify inhibitors as potentially new antifungal compounds.
... The above chemistries are but a sampling of the available enzymes that may eventually find applicability in NP bioconjugation. Similar to BirA and LplA, phosphopantetheinyl transferase (PPTase) reacts with a short peptide sequence (70-90 residues) referred to as the acyl carrier protein (ACP) which can be directly incorporated into proteins of interest [58]. PPTase transfers 4 0 -phosphopantetheine from coenzyme A to a reactive serine of the ACP sequence. ...
... 28 Various CoA analogs have been prepared by this method and employed as inhibitors or mechanistic probes to investigate CoA-dependent enzymes. 23,25,[29][30][31][32][33] The final compounds were isolated by reverse-phase HPLC in reasonable yields and characterized by 1 H, 13 C, and 31 P NMR and HRMS. ...
Polyhydroxybutyrate (PHB) synthases (PhaCs) catalyze the formation of biodegradable PHB polymers that are considered as an ideal alternative to petroleum-based plastics. To provide strong evidence for the preferred mechanistic model involving covalent and noncovalent intermediates, a substrate analog HBOCoA was synthesized chemoenzymatically. Substitution of sulfur in native substrate HBCoA with an oxygen in HBOCoA enabled detection of (HB)nOCoA (n = 2-6) intermediates when the polymerization was catalyzed by wild-type (wt-)PhaECAv at 5.84 hr(-1). This extremely slow rate is due to thermodynamically unfavorable steps that involve formation of enzyme-bound PHB species (thioesters) from corresponding CoA oxoesters. Synthesized standards (HB)nOCoA (n = 2-3) were found to undergo both reacylation and hydrolysis catalyzed by the synthase. Distribution of the hydrolysis products highlights the importance of penultimate ester group as previously suggested. Additionally, the reaction between primed synthase [(3)H]-sT-PhaECAv and HBOCoA yielded [(3)H]-sTet-O-CoA at a rate constant faster than 17.4 s(-1), which represents the first example that a substrate analog undergoes PHB chain elongation at a rate close to the native substrate (65.0 s(-1)). Therefore, for the first time with a wt-synthase, strong evidence was obtained to support the chain elongation model involving covalent and noncovalent intermediates.
... Acyl-ACPs were prepared from acyl-CoAs and apo-ACP by means of the B. subtilis Sfp phosphopantetheinyl transferase enzyme. 30,35,36 The transferase reaction mixture (2 mL) contained 50 mM Tris-HCl pH 6.8, 10 mM magnesium chloride, 750 μM apo-ACP, 937 μM acyl-CoA (1.25× apo-ACP), and 3 μM Sfp. During the preparation of long-chain acyl-ACPs (carbon chain lengths greater than eight), precipitates formed in the reaction mixture prevented the reaction from proceeding to completion. ...
The acyl-homoserine lactone (AHL) autoinducer mediated quorum sensing regulates virulence in several pathogenic bacteria. The hallmark of an efficient quorum sensing system relies on the tight specificity in signal generated by each bacterium. Since AHL signal specificity is derived from the acyl-chain of acyl-ACP substrate, AHL synthase enzymes must recognize and react with the native acyl-ACP with high catalytic efficiency while keeping reaction rates with non-native acyl-ACPs low. The mechanism of acyl-ACP substrate recognition in these enzymes however, remains elusive. In this study, we investigated differences in catalytic efficiencies for shorter and longer chain acyl-ACP substrates reacting with an octanoyl-homoserine lactone synthase, Burkholderia mallei BmaI1. With the exception of two-carbon shorter hexanoyl-ACP, the catalytic efficiencies of butyryl-ACP, decanoyl-ACP and octanoyl-CoA reacting with BmaI1 decreased by greater than 20-fold compared to the native octanoyl-ACP substrate. Furthermore, we also noticed kinetic cooperativity when BmaI1 reacted with non-native acyl-donor substrates. Our kinetic data suggest that non-native acyl-ACP substrates are unable to form a stable and productive BmaI1.acyl-ACP.SAM ternary complex and are thus effectively discriminated by the enzyme. These results offer insights into the molecular basis of substrate recognition for the BmaI1 enzyme.
... It exhibits a broad promiscuity toward CoA derivatives and carrier proteins. Hence, it is frequently used in biotechnological approaches to load carrier proteins with ppan conjugated with molecules such as amino acids (Belshaw et al., 1999), peptides (Sieber et al., 2003), fatty acids (Kosa et al., 2012), and fluorescent labels (La Clair et al., 2004). ...
Phosphopantetheine transferases represent a class of enzymes found throughout all forms of life. From a structural point of view, they are subdivided into three groups, with transferases from group II being the most widespread. They are required for the posttranslational modification of carrier proteins involved in diverse metabolic pathways. We determined the crystal structure of the group II phosphopantetheine transferase Sfp from Bacillus in complex with a substrate carrier protein in the presence of coenzyme A and magnesium, and observed two protein-protein interaction sites. Mutational analysis showed that only the hydrophobic contacts between the carrier protein's second helix and the C-terminal domain of Sfp are essential for their productive interaction. Comparison with a similar structure of a complex of human proteins suggests that the mode of interaction is highly conserved in all domains of life.
Nature uses a diverse array of protein post‐translational modifications (PTMs) to regulate protein structure, activity, localization, and function. Among them, protein 4′‐phosphopantetheinylation derived from coenzyme A (CoA) is an essential PTM for the biosynthesis of fatty acids, polyketides, and nonribosomal peptides in prokaryotes and eukaryotes. To explore its functions, various chemical probes mimicking the natural structure of 4′‐phosphopantetheinylation have been developed. In this minireview, we summarize these chemical probes and describe their applications in direct and metabolic labeling of proteins in bacterial and mammalian cells.
The design and construction of crystalline protein arrays to selectively assemble ordered nanoscale materials has potential applications in sensing, catalysis and medicine. Whereas numerous designs have been implemented for the bottom-up construction of novel protein assemblies, the generation of artificial functional materials has been relatively unexplored. Enzyme-directed post-translational modifications are responsible for the functional diversity of the proteome and thus, could be harnessed to selectively modify artificial protein assemblies. In this study, we describe the use of phosphopantetheinyl transferases (PPTases), a class of enzymes that covalently modify proteins using coenzyme A (CoA), to site-selectively tailor the surface of designed, two-dimensional (2D) protein crystals. We demonstrate that a short peptide (ybbR) or a molecular tag (CoA) can be covalently tethered to 2D arrays to enable enzymatic functionalization using Sfp PPTase. The site-specific modification of two different protein array platforms is facilitated by PPTases to afford both small-molecule- and protein-functionalized surfaces with no loss in crystalline order. This work highlights the potential for chemoenzymatic modification of large protein surfaces towards the generation of sophisticated protein platforms reminiscent of the complex landscape of cell surfaces.
Covalent modification of proteins is extensively used in research and industry for biosensing, medical diagnostics, targeted drug delivery, and many other practical applications. The conventional method for production of protein conjugates has changed little in the last 20 years mostly relying on reactions of side chains of cysteine and lysine residues. Due to the presence of large numbers of similar reactive amino acid residues in proteins, common synthetic methods generally produce complex mixtures of products, which are difficult to separate. An emerging alternative technology for covalent modification of proteins involves formation of a covalent bond with a hexahistidine affinity tag present in a majority of recombinant proteins without interfering with other amino acid residues. The approach is based on formation of a ternary complex of the hexahistidine sequence with a bivalent metal cation chelated by ligand bearing an electrophilic Baylis-Hillman ester group capable of subsequent formation of a covalent bond with one of the histidine residues of the tag. The reaction proceeds under mild reaction conditions in neutral aqueous solutions under high dilutions (10⁻⁵ to 10⁻⁴ M) providing a stable covalent bond between the label and an imidazole residue in a hexahistidine tag at either C- or N-terminus. Because hexahistidine affinity tag methodology is a de-facto standard for preparation of recombinant proteins our approach can be easily implemented for selective derivatization of these proteins with fluorescent groups, alkynyl groups for “click” reactions, or biotinylation.
4′-Phosphopantetheinyl transferases (PPTases) have been employed by researchers as versatile biocatalysts for the site-specific modification of numerous protein targets with structurally diverse molecules. Here we describe the use of these enzymes for the production of homogeneous antibody–drug conjugates (ADCs), which have garnered much attention as innovative anticancer drugs. The exceptionally broad substrate tolerance of PPTases allows for one-step and two-step conjugation strategies for site-specific ADC synthesis. While one-step conjugation involves direct coupling of a drug molecule to an antibody, two-step conjugation provides increased flexibility and efficiency of the conjugation process by first attaching a bioorthogonal chemical handle that is then used for drug molecule attachment in a second step. The aim of this chapter is to outline detailed protocols for both labeling procedures, as well as to provide guidance on enzyme and substrate preparation.
Natural products (NPs) are a major source of compounds for the medical, agricultural and biotechnological industry. Many of these compounds are of microbial origin, and in particular from Actinobacteria or filamentous fungi. To successfully identify novel compounds that correlate to a bioactivity of interest, or discover new enzymes with desired functions, systematic multi‐omics approaches have been developed over the years. Bioinformatics tools harness the rapidly expanding wealth of genome sequence information, revealing previously unsuspected biosynthetic diversity. Varying growth conditions or application of elicitors are applied to activate cryptic biosynthetic gene clusters, and metabolomics provide detailed insights into the NPs they specify. Combining these technologies with proteomics‐based approaches to profile the biosynthetic enzymes provides scientists with insights into the full biosynthetic potential of microorganisms. The proteomics approaches include enrichment strategies such as employing activity‐based probes designed by chemical biology, as well as unbiased (quantitative) proteomics methods. In this review, we discuss the opportunities and challenges in microbial NP research, and in particular the application of proteomics to link biosynthetic enzymes to the molecules they produce, and vice versa.
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Natural products from the human microbiota may mediate host health and disease. However, discovery of the biosynthetic gene clusters that generate these metabolites has far outpaced identification of the molecules themselves. Here, we used an isolation-independent approach to access the probable products of a nonribosomal peptide synthetase-encoding gene cluster from Ruminococcus bromii, an abundant gut commensal bacterium. By combining bioinformatics with in vitro biochemical characterization of biosynthetic enzymes, we predicted that this pathway likely generates an N-acylated dipeptide aldehyde (ruminopeptin). We then used chemical synthesis to access putative ruminopeptin scaffolds. Several of these compounds inhibited Staphylococcus aureus endoproteinase GluC (SspA/V8 protease). Homologs of this protease are found in gut commensals and opportunistic pathogens as well as human gut metagenomes. Overall, this work reveals the utility of isolation-independent approaches for rapidly accessing bioactive compounds and highlights a potential role for gut microbial natural products in targeting gut microbial proteases.
The structural diversity and complexity of marine natural products have made them a rich and productive source of new bioactive molecules for drug development. The identification of these new compounds has led to extensive study of the protein constituents of the biosynthetic pathways from the producing microbes. Essential processes in the dissection of biosynthesis have been the elucidation of catalytic functions and the determination of 3D structures for enzymes of the polyketide synthases and nonribosomal peptide synthetases that carry out individual reactions. The size and complexity of these proteins present numerous difficulties in the process of going from gene to structure. Here, we review the problems that may be encountered at the various steps of this process and discuss some of the solutions devised in our and other labs for the cloning, production, purification, and structure solution of complex proteins using Escherichia coli as a heterologous host.
Non-ribosomal peptide synthetase (NRPS) machineries produce many medically relevant peptides that cannot be easily accessed by chemical synthesis. Thus, understanding NRPS mechanism is of crucial importance to allow efficient redesign of these machineries in order to produce new compounds. During NRPS-mediated synthesis, substrates are covalently attached to PCPs, and studies of NRPSs are impeded by difficulties in producing PCPs loaded with substrates. Different approaches to load substrates on to PCP domains have been described, but all suffer from difficulties in either the complexity of chemical synthesis or low enzymatic efficiency. Here, we describe an enhanced chemo-enzymatic loading method that combines two approaches into a single, highly efficient one-pot loading reaction. First, D-pantetheine and ATP are converted into dephospho-coenzyme A via the actions of two enzymes from coenzyme A (CoA) biosynthesis. Next, phosphoadenylates are dephosphorylated using alkaline phosphatase to allow linker attachment to PCP domain by Sfp mutant R4-4, which is inhibited by phosphoadenylates. This route does not depend on activity of the commonly problematic dephospho-CoA kinase, and therefore offers an improved method for substrate loading onto PCP domains.
Bacteria use chemical molecules called autoinducers as votes to poll their numerical strength in a colony. This polling mechanism, commonly referred to as quorum sensing, enables bacteria to build a social network and provide a collective response for fighting off common threats. In Gram-negative bacteria, AHL synthases synthesize acyl-homoserine lactone (AHL) autoinducers to turn on the expression of several virulent genes including biofilm formation, protease secretion, and toxin production. Therefore, inhibiting AHL signal synthase would limit quorum sensing and virulence. In this chapter, we describe four enzymatic methods that could be adopted to investigate a broad array of AHL synthases. The enzymatic assays described here should accelerate our mechanistic understanding of quorum-sensing signal synthesis that could pave the way for discovery of potent antivirulence compounds.
Nonribosomal peptide synthetases (NRPSs) are large multienzyme machineries that assemble numerous peptides with large structural and functional diversity. These peptides include more than 20 marketed drugs, such as antibacterials (penicillin, vancomycin), antitumor compounds (bleomycin), and immunosuppressants (cyclosporine). Over the past few decades biochemical and structural biology studies have gained mechanistic insights into the highly complex assembly line of nonribosomal peptides. This Review provides state-of-the-art knowledge on the underlying mechanisms of NRPSs and the variety of their products along with detailed analysis of the challenges for future reprogrammed biosynthesis. Such a reprogramming of NRPSs would immediately spur chances to generate analogues of existing drugs or new compound libraries of otherwise nearly inaccessible compound structures.
Nicht-ribosomale Peptidsynthetasen (NRPSs) sind große Multienzymmaschinerien, die zahlreiche Peptide mit enormer struktureller und funktionaler Diversität erzeugen. Unter diesen Produkten befinden sich mehr als 20 auf dem Markt befindliche Wirkstoffe, darunter Antibiotika (Penicillin, Vancomycin), antitumorale Medikamente (Bleomycin) und Immunsuppressiva (Cyclosporin). In den vergangenen Jahrzehnten haben biochemische sowie strukturbiologische Studien mechanistische Einblicke in die hochkomplexen NRPSs gewährt. Dieser Aufsatz fasst den aktuellen Kenntnisstand über die zugrundeliegenden Mechanismen von NRPSs zusammen und gibt einen Überblick über die Vielfalt ihrer Produkte. Ebenso behandelt werden die Probleme und Herausforderungen, die mit der Umprogrammierung von NRPS-Systemen einhergehen. Das Potenzial einer solchen Umprogrammierung liegt begründet in einer nachhaltigen Generierung von Wirkstoffanaloga und neuen Substanzbibliotheken, die anderenfalls kaum zugänglich sind.
The fields of chemical biology and bioorthogonal chemistry have led to significant advances in the study of cellular biomolecules. This chapter focuses on enzyme-based bioorthogonal strategies for the labeling of cellular proteins along with those that are expressed and subsequently modified in vitro where relevant. It highlights some prominent enzymatic labeling methods with both in vivo and in vitro applications. Enzymatic labeling of biomolecules relies on the presence of a cellular enzyme, either endogenous or recombinant, to facilitate the attachment of an abiotic or other reagents to a target protein. The chapter also talks about several enzyme systems that have been manipulated to achieve the requisite bioorthogonal labeling of proteins. Self-labeling enzymes and proteins directly attach substrates and reagents to an amino acid or functional group within their structure rather than an exogenous target biomolecule or substrate. Biarsenical Dyes and SpyCatcher/SpyTag are some alternate methods of protein labeling.
Derivatization of a 5′-(vinylsulfonylaminodeoxy)adenosine scaffold with a clickable functionality provided an activity-based probe that was used to label native carrier protein (CP) motifs in nonribosomal peptide synthetases (NRPSs). When coupled with a fluorescent tag, this probe selectively targeted phosphopantetheinylated CPs (holo-form) from recombinant NRPS enzyme systems and in whole proteomes.
Diversity in non-ribosomal peptide and polyketide secondary metabolism is facilitated by interaction between biosynthetic domains with discrete monomer loading and their cognate tailoring enzymes, such as oxidation or halogenation enzymes. The cooperation between peptidyl carrier proteins and flavin-dependent enzymes offers a specialized strategy for monomer selectivity, which oxidizes small molecules from within a complex cellular milieu. In an effort to study this process, we have developed fluorescent probes to selectively label aerobic flavin-dependent enzymes. Here we report the preparation and implementation of these tools to label oxidase, monooxygenase and halogenase flavin-dependent enzymes.
An ideal target for metabolic engineering, fatty acid biosynthesis remains poorly understood on a molecular level. These carrier protein dependent pathways require fundamental protein • protein interactions to guide reactivity and processivity, and their control has become one of the major hurdles in successfully adapting these biological machines. Our laboratory has developed methods to prepare acyl carrier proteins (ACPs) loaded with substrate mimetics and crosslinkers to visualize and trap interactions with partner enzymes, and we continue to expand the tools for studying these pathways. We now describe application of the slow-onset, tight-binding inhibitor triclosan to explore the interactions between the type II fatty acid ACP from Escherichia coli, AcpP, and its corresponding enoyl-ACP reductase, FabI. We show that the AcpP • triclosan complex demonstrates nM binding, inhibits in vitro activity and can be used to isolate FabI in complex proteomes.
Coenzyme A (CoA) and its thioesters play a diverse array of roles in biologic systems. The enzymes that catalyze reactions of CoA are of interest for a variety of reasons, including, but not limited to, their potential as drug targets. The enzymology of CoA biosynthesis is now well understood, and the genes for all of the enzymes involved have been identified. Thioesters are inherently reactive toward acyl transfer reactions and toward reactions involving deprotonation of the α-carbon, and these are the primary reactivity patterns in enzyme-catalyzed reactions of CoA thioesters. CoA utilizing enzymes have been widely studied mechanistically and structurally. Analogs of the natural CoA thioester substrates have been widely used in these studies, including thioesters of unnatural or uncommon acyl groups as well as a large number of analogs in which the thioester is replaced with alternative functionality. Recent technical applications of CoA have included the tagging of carrier protein domains and carrier protein fusions with tagged phosphopantetheine derivatives transferred enzymatically from the corresponding tagged CoA derivatives using promiscuous phosphopantetheinyl transferases.
Posttranslational modifications diversify the limited amino acid pool, expanding 20 amino acids into a possibly limitless number of residues. These modifications are catalyzed by a large family of proteins specific to each modification. This chapter focuses on the function of common posttranslational modifications and highlights work done in the last 4 years (2005–08). Many of the modifications are needed for cell growth, transcriptional regulation, and metabolism. In other words, posttranslational modifications are required for everyday activity. Modifications covered include phosphorylation, sulfation, disulfide formation, methylation, N-acetylation, hydroxylation, glycosylation, ADP-ribosylation, prenylation, and tethering of biotin, lipoate, and phosphopantetheine. Here, we look at the functions that the modifications play in mammalian, plant, and bacterial systems as well as in virus production.
Coenzyme A (CoA) is a ubiquitous and essential cofactor that is involved in a large proportion of all central metabolic reactions. In most of these reactions, the cofactor acts as an acyl carrier, and either activates the acyl group for group transfer or electrophilic attack, or increases the acidity of the protons adjacent to the carbonyl to facilitate the formation of a nucleophilic enolate. This chapter describes the discovery of CoA and the early studies on its biosynthesis and enzymology, and the current status of our knowledge of its universal five-step biosynthetic pathway from pantothenic acid (vitamin B5) – including an overview of the variations in the pathway across sequenced genomes, and of the data on the essentiality of the genes encoding the CoA biosynthetic enzymes. This chapter also discusses CoA enzymology, with a special focus on enzymes that consume, degrade, and recycle CoA, on enzymes that biosynthesize CoA thioesters, and on enzymes that subsequently use these thioesters for group transfer reactions. The enzymology of proteins that act in the Claisen condensation of CoA thioesters (and the retro-Claisen cleavage reactions), is also described. Finally, an overview of the use of CoA analogues in biotechnological applications and in the design and development of drugs and enzyme inhibitors is provided.
Microbial synthesis of value-added compounds often depends upon the creation or introduction of heterologous metabolic pathways into production hosts. However, there are many challenges in the engineering of a pathway and even more issues in optimizing it for the highest product yield. In this chapter, we will review a wide variety of computational and experimental tools that have been developed to design, construct, and optimize metabolic pathways. In addition, we will illustrate the applications of these tools in synthetic biology by highlighting the engineering of three metabolic pathways involved in the synthesis of glucaric acid, 1,4-butanediol, and 1,3-propanediol.
Genetic approaches have greatly contributed to our understanding of nonribosomal peptide biosynthetic machinery; however, proteomic investigations are limited. Here, we developed a highly sensitive detection strategy for multidomain nonribosomal peptide synthetases (NRPSs) by using a multiple-labeling technique with active-site-directed probes for adenylation domains. When applied to gramicidin S-producing and -nonproducing strains of Aneurinibacillus migulanus (DSM 5759 and DSM 2895, respectively), the multiple technique sensitively detected an active multidomain NRPS (GrsB) in lysates obtained from the organisms. This functional proteomics method revealed an unknown inactive precursor (or other inactive form) of GrsB in the nonproducing strain. This method provides a new option for the direct detection, functional analysis, and high-resolution identification of low-abundance active NRPS enzymes in native proteomic environments.
This chapter lists the CAS registry number, chemical structure, chemical abstract (CA) index name, other chemical names, chemical/dye class, synthesis procedure, molecular formula, and molecular weight of YO-PRO 1. Other properties listed for this fluorescent dye include the physical form, solubility, melting point, boiling point, pKa, absorption maxima, emission maxima, molar extinction coefficient and quantum yield. The chapter also includes references on the use, properties, and safety/toxicity of YO-PRO 1. It presents a list of imaging/labeling applications, biological/medical applications and industrial applications of YO-PRO 1.
Of the many tools in use to characterize natural products and their biosynthetic machinery, mass spectrometry (MS) is rapidly becoming one of the most essential. The importance of MS is highlighted by the fact that scientific journals are unlikely to accept the characterization of a new natural product without the inclusion of MS data. Within the general biosynthetic natural products community, the creative use of MS has been minimal, and in many cases, MS analysis is carried out only after the majority of the activities within the biosynthetic pathway have been determined by other means. In recent years, this trend has begun to change as more advanced, yet more user-friendly, mass spectrometers are made commercially available. Although the improvements in instrument capacity and design are driven in large part by the clinical ‘omics’ community, these changes have allowed MS to move to the forefront of natural products chemistry. Current methods and applicationis used to study both polyketide and nonribosomal peptide biosynthetic pathways will be the focus of this chapter, in particular utilization of the phosphopantetheinyl ejection assay to determine the specific functions of various components of natural biosynthetic pathways. This chapter will also provide a preview of up-and-coming advances in MS analysis of natural products biosynthesis.
Evaluation of new acyl carrier protein hydrolase (AcpH, EC 3.1.4.14) homologs from proteobacteria and cyanobacteria reveals significant variation in substrate selectivity and kinetic parameters for phosphopantetheine hydrolysis from carrier proteins. Evaluation with carrier proteins from both primary and secondary metabolic pathways reveals an overall preference for acyl carrier protein (ACP) substrates from type II fatty acid synthases, as well as variable activity for polyketide synthase ACPs and peptidyl carrier proteins (PCP) from non-ribosomal peptide synthases. We also demonstrate the kinetic parameters of these homologs for AcpP and the 11-mer peptide substrate YbbR. These findings enable the fully reversible labeling of all three classes of natural product synthase carrier proteins as well as full and minimal fusion protein constructs.
This chapter describes structural and associated enzymological studies of polyketide synthases. The sequence-structure-function relationship of polyketide biosynthesis, compared with homologous fatty acid synthesis, is discussed in detail. The structural and functional studies shed light on sequence and structural motifs important for the timing, substrate recognition, enzyme catalysis and protein-protein interactions leading to the extraordinary structural diversity of naturally-occurring polyketides.
Phosphopantetheinyl transferases (PPTase) Sfp and AcpS catalyze a highly efficient reaction that conjugates chemical probes of diverse structures to proteins. PPTases have been widely used for site-specific protein labeling and live cell imaging of the target proteins. Here we describe the use of PPTase-catalyzed protein labeling in protein engineering by facilitating high-throughput phage selection.
The mechanistic details of many polyketide synthases (PKSs) remain elusive due to the instability of transient intermediates that are not accessible via conventional methods. Here we report an atom replacement strategy that enables the rapid preparation of polyketone surrogates by selective atom replacement, thereby providing key substrate mimetics for detailed mechanistic evaluations. Polyketone mimetics are positioned on the actinorhodin acyl carrier protein (actACP) to probe the underpinnings of substrate association upon nascent chain elongation and processivity. Protein NMR is used to visualize substrate interaction with the actACP, where a tetraketide substrate is shown not to bind within the protein, while heptaketide and octaketide substrates show strong association between helix II and IV. To examine the later cyclization stages, we extended this strategy to prepare stabilized cyclic intermediates and evaluate their binding by the actACP. Elongated monocyclic mimics show much longer residence time within actACP than shortened analogs. Taken together, these observations suggest ACP-substrate association occurs both before and after ketoreductase action upon the fully elongated polyketone, indicating a key role played by the ACP within PKS timing and processivity. These atom replacement mimetics offer new tools to study protein and substrate interactions and are applicable to a wide variety of PKSs.
Polyhydroxyalkanoate (PHA) synthases (PhaCs) catalyze the formation of biodegradable PHAs that are considered to be ideal alternatives to non-biodegradable synthetic plastics. However, study of PhaCs has been challenging because the rate of PHA chain elongation is much faster than that of initiation. This difficulty, along with lack of a crystal structure, has become the main hurdle to understanding and engineering PhaCs for economical PHA production. Here we report the synthesis of two carbadethia CoA analogues-sT-CH2 -CoA (26 a) and sTet-CH2 -CoA (26 b)-as well as sT-aldehyde (saturated trimer aldehyde, 29), as new PhaC inhibitors. Study of these analogues with PhaECAv revealed that 26 a/b and 29 are competitive and mixed inhibitors, respectively. Both the CoA moiety and extension of PHA chain will increase binding affinity; this is consistent with our docking study. Estimation of the Kic values of 26 a and 26 b predicts that a CoA analogue incorporating an octameric hydroxybutanoate (HB) chain might facilitate the formation of a kinetically well-behaved synthase.
Fatty acid-derived ether lipids are present not only in most vertebrates but also in some bacteria. Here we describe what is to our knowledge the first gene cluster involved in the biosynthesis of such lipids in myxobacteria that encodes the multifunctional enzyme ElbD, which shows similarity to polyketide synthases. Initial characterization of elbD mutants in Myxococcus xanthus and Stigmatella aurantiaca showed the importance of these ether lipids for fruiting body formation and sporulation.
A method has been devised for the electrophoretic transfer of proteins from polyacrylamide gels to nitrocellulose sheets. The method results in quantitative transfer of ribosomal proteins from gels containing urea. For sodium dodecyl sulfate gels, the original band pattern was obtained with no loss of resolution, but the transfer was not quantitative. The method allows detection of proteins by autoradiography and is simpler than conventional procedures. The immobilized proteins were detectable by immunological procedures. All additional binding capacity on the nitrocellulose was blocked with excess protein; then a specific antibody was bound and, finally, a second antibody directed against the first antibody. The second antibody was either radioactively labeled or conjugated to fluorescein or to peroxidase. The specific protein was then detected by either autoradiography, under UV light, or by the peroxidase reaction product, respectively. In the latter case, as little as 100 pg of protein was clearly detectable. It is anticipated that the procedure will be applicable to analysis of a wide variety of proteins with specific reactions or ligands.
The multifunctional 6-methylsalicylic acid synthase gene from Penicillium patulum was engineered for regulated expression in Streptomyces coelicolor. Production of significant amounts of 6-methylsalicylic acid by the recombinant strain was proven by nuclear magnetic resonance spectroscopy. These results suggest that it is possible to harness the molecular diversity of eukaryotic polyketide pathways by heterologous expression of biosynthetic genes in an easily manipulated model bacterial host in which prokaryotic aromatic and modular polyketide synthase genes are already expressed and recombined.
Polyketides are an extensive class of secondary metabolites with diverse molecular structures and biological activities. A plasmid-based multicomponent polyketide synthase expression cassette was constructed using a subset of actinorhodin (act) biosynthetic genes (actI-orf1, actI-orf2, actI-orf3, actIII, actVII, and actIV) from Streptomyces coelicolor which specify the construction of the anthraquinone product aloesaponarin II, a molecule derived from acetyl coenzyme A and 7 malonyl coenzyme A extender units. This system was designed as an indicator pathway in Streptomyces parvulus to quantify polyketide product formation and to examine the functional significance of specific polyketide synthase components, including the act beta-ketoacyl synthase (beta-KS; encoded by actI-orf1 and actI-orf2) and the act cyclase/dehydrase (encoded by actVII-orf4). Site-directed mutagenesis of the putative active site Cys (to a Gln) in the actI-orf1 beta-KS product completely abrogated aloesaponarin II production. Changing the putative acyltransferase active-site Ser (to a Leu) located in the actI-orf1 beta-KS product led to significantly reduced but continued production of aloesaponarin II. Replacement of the expression cassette with one containing a mutant form of actI-orf2 gave no production of aloesaponarin II or any other detectable polyketide products. However, an expression cassette containing a mutant form of actVII-orf4 gave primarily mutactin with low-level production of aloesaponarin II.
In nonribosomal biosynthesis of peptide antibiotics by multimodular synthetases, amino acid monomers are activated by the
adenylation domains of the synthetase and loaded onto the adjacent carrier protein domains as thioesters, then the formation
of peptide bonds and translocation of the growing chain are effected by the synthetase's condensation domains. Whether the
condensation domains have any editing function has been unknown. Synthesis of aminoacyl–coenzyme A (CoA) molecules and direct
enzymatic transfer of aminoacyl-phosphopantetheine to the carrier domains allow the adenylation domain editing function to
be bypassed. This method was used to demonstrate that the first condensation domain of tyrocidine synthetase shows low selectivity
at the donor residue (d-phenylalanine) and higher selectivity at the acceptor residue (l-proline) in the formation of the chain-initiating d-Phe-l-Pro dipeptidyl-enzyme intermediate.
The acyl carrier proteins (ACPs) of fatty acid synthase and polyketide synthase as well as peptidyl carrier proteins (PCPs)
of nonribosomal peptide synthetases are modified by 4′-phosphopantetheinyl transferases from inactiveapo-enzymes to their active holo forms by transferring the 4′-phosphopantetheinyl moiety of coenzyme A to a conserved serine residue of the carrier protein.
4′-Phosphopantetheinyl transferases have been classified into two types; the AcpS type accepts ACPs of fatty acid synthase
and some ACPs of type II polyketide synthase as substrates, whereas the Sfp type exhibits an extraordinarily broad substrate
specificity. Based on the previously published co-crystal structure of Bacillus subtilis AcpS and ACP that provided detailed information about the interacting residues of the two proteins, we designed a novel hybrid
PCP by replacing the Bacillus brevis TycC3-PCP helix 2 with the corresponding helix of B. subtilis ACP that contains the interacting residues. This was performed for the PCP domain as a single protein as well as for the
TycA-PCP domain within the nonribosomal peptide synthetase module TycA from B. brevis. Both resulting proteins, designated hybrid PCP (hPCP) and hybrid TycA (hTycA), were modified in vivo during heterologous expression in Escherichia coli (hPCP, 51%; hTycA, 75%) and in vitro with AcpS as well as Sfp to 100%. The designated hTycA module contains two other domains: an adenylation domain (activating
phenylalanine to Phe-AMP and afterward transferring the Phe to the PCP domain) and an epimerization domain (converting the
PCP-bound l-Phe to d-Phe). We show here that the modified PCP domain of hTycA communicates with the adenylation domain and that the co-factor
of holo-hPCP is loaded with Phe. However, communication between the hybrid PCP and the epimerization domain seems to be disabled.
Nevertheless, hTycA is recognized by the next proline-activating elongation module TycB1in vitro, and the dipeptide is formed and released as diketopiperazine.
To further explore possible avenues for accessing microbial biodiversity for drug discovery from natural products, we constructed
and screened a 5,000-clone “shotgun” environmental DNA library by using an Escherichia coli-Streptomyces lividans shuttle cosmid vector and DNA inserts from microbes derived directly (without cultivation) from soil. The library was analyzed
by several means to assess diversity, genetic content, and expression of heterologous genes in both expression hosts. We found
that the phylogenetic content of the DNA library was extremely diverse, representing mostly microorganisms that have not been
described previously. The library was screened by PCR for sequences similar to parts of type I polyketide synthase genes and
tested for the expression of new molecules by screening of live colonies and cell extracts. The results revealed new polyketide
synthase genes in at least eight clones. In addition, at least five additional clones were confirmed by high-pressure liquid
chromatography analysis and/or biological activity to produce heterologous molecules. These data reinforce the idea that exploiting
previously unknown or uncultivated microorganisms for the discovery of novel natural products has potential value and, most
importantly, suggest a strategy for developing this technology into a realistic and effective drug discovery tool.
The ery A region of the erythromycin biosynthetic gene cluster of Saccharopolyspora erythraea has previously been shown to contain three large open reading frames (ORFs) that encode the components of 6-deoxyerythronolide B synthase (DEBS). Polyclonal antibodies were raised against recombinant proteins obtained by overexpression of 3' regions of the ORF2 and ORF3 genes. In Western blotting experiments, each antiserum reacted strongly with a different high molecular weight protein in extracts of erythromycin-producing S. erythraea cells. These putative DEBS 2 and DEBS 3 proteins were purified and subjected to N-terminal sequence analysis. The protein sequences were entirely consistent with the and DEBS 3 proteins were purified and subjected to N-terminal sequence analysis. The protein sequences were entirely consistent with the translation start sites predicted from the DNA sequences of ORFs 2 and 3. A third high molecular weight protein co-purified with DEBS 2 and DEBS 3 and had an N-terminal sequence that matched a protein sequence translated from the DNA sequence some 155 base pairs upstream from the previously proposed start codon of ORF1.
The preparation of a number of agarose and polyacrylamide bead derivatives useful in the purification of proteins by affinity
chromatography is described. These techniques permit (a) the attachment of ligands to the gel through extended hydrocarbon chains which place the ligand at varying distances from
the gel matrix backbone; (b) the covalent attachment of ligands to agarose or polyacrylamide gels through amino, carboxyl, phenolic, or imidazole groups
of the ligand; and (c) the preparation of adsorbents containing ligands attached by bonds which are susceptible to specific chemical cleavage,
thus providing means of removing the intact protein-ligand complex from the affinity adsorbent. It is demonstrated that successful
application of affinity chromatography in many cases will critically depend on placing the ligand at a considerable distance
from the matrix backbone. Techniques are also described which provide important approaches and considerations in the insolubilization
of peptides and proteins to agarose and polyacrylamide.
N-ethylmaleimide (NEM) inhibits lactose uptake in E. coli by reacting with the M protein component of the lac permease system. In an attempt to estimate the distance between the NEM reactive site and the substrate binding site, we have synthesized a beta-galactoside with NEM as the aglycon moiety (NEM-gal). NEM-gal was a more effective inhibitor of lactose transport than was NEM. Part of the inhibition by NEM-gal was caused by competition with lactose for the substrate binding site. To estimate this part of the inhibition, we synthesized the saturated and thus the unreactive N-ethylsuccinimide (NES) analog of NEM-gal. Nes-gal was a competitive inhibitor of lactose uptake. The remainder of the inhibition by NEM-gal followed first-order kinetics with the same rate constant as NEM. In addition, the protective effect of thiodigalactoside against the inhibition of transport by NEM was also observed against irreversible inhibition by NEM-gal. We suggest that the reactivity of NEM was unaltered by bringing it near the beta-galactoside binding site by way of covalent attachment to galactose. We conclude that the distance between the NEM reactive site and the position of the glycosidic oxygen of beta-galactosides bound to the lactose site is greater than 8 A.
Macrocyclic polyketides have been subjects of great interest in synthetic and biosynthetic chemistry because of their structural complexity and medicinal activities. With expression of the entire 6-deoxyerythronolide B synthase (DEBS) (10,283 amino acids) in a heterologous host, substantial quantities of 6-deoxyerythronolide B (6dEB), the aglycone of the macrolide antibiotic erythromycin, and 8,8a-deoxyoleandolide, a 14-membered lactone ring identical to 6dEB except for a methyl group side chain in place of an ethyl unit, were synthesized in Streptomyces coelicolor. The biosynthetic strategy utilizes a genetic approach that facilitates rapid structural manipulation of DEBS or other modular polyketide synthases (PKSs), including those found in actinomycetes with poorly developed genetic methods. From a technological viewpoint, this approach should allow the rational design of biosynthetic products and may eventually lead to the generation of diverse polyketide libraries by means of combinatorial cloning of naturally occurring and mutant PKS modules.
Background:
All polyketide synthases, fatty acid synthases, and non-ribosomal peptide synthetases require posttranslational modification of their constituent acyl carrier protein domain(s) to become catalytically active. The inactive apoproteins are converted to their active holo-forms by posttranslational transfer of the 4'-phosphopantetheinyl (P-pant) moiety of coenzyme A to the sidechain hydroxyl of a conserved serine residue in each acyl carrier protein domain. The first P-pant transferase to be cloned and characterized was the recently reported Escherichia coli enzyme ACPS, responsible for apo to holo conversion of fatty acid synthase. Surprisingly, initial searches of sequence databases did not reveal any proteins with significant peptide sequence similarity with ACPS.
Results:
Through refinement of sequence alignments that indicated low level similarity with the ACPS peptide sequence, we identified two consensus motifs shared among several potential ACPS homologs. This has led to the identification of a large family of proteins having 12-22 % similarity with ACPS, which are putative P-pant transferases. Three of these proteins, E. coli EntD and o195, and B. subtilis Sfp, have been overproduced, purified and found to have P-pant transferase activity, confirming that the observed low level of sequence homology correctly predicted catalytic function. Three P-pant transferases are now known to be present in E. coli (ACPS, EntD and o195); ACPS and EntD are specific for the activation of fatty acid synthase and enterobactin synthetase, respectively. The apo-protein substrate for o195 has not yet been identified. Sfp is responsible for the activation of the surfactin synthetase.
Conclusions:
The specificity of ACPS and EntD for distinct P-pant-requiring enzymes suggests that each P-pant-requiring synthase has its own partner enzyme responsible for apo to holo activation of its acyl carrier domains. This is the first direct evidence that in organisms containing multiple P-pant-requiring pathways, each pathway has its own posttranslational modifying activity.
Definitions of 'marine biotechnology' often refer to the vast potential of the oceans to lead to new cures for human and animal disease; the exploitation of natural drugs has always been the most basic form of biotechnology. Although only initiated in the late 1970s, natural drug discovery from the world's oceans has been accelerated by the chemical uniqueness of marine organisms and by the need to develop drugs for contemporary, difficult to cure, diseases. Current research activities, while primarily within the academic laboratories, have generated convincing evidence that marine drug discovery has an exceedingly bright future.
The polyketides are a diverse group of natural products with great significance as human and veterinary pharmaceuticals. A significant barrier to the production of novel genetically engineered polyketides has been the lack of available heterologous expression systems for functional polyketide synthases (PKSs). Herein, we report the expression of an intact functional PKS in Escherichia coli and Saccharomyces cerevisiae. The fungal gene encoding 6-methylsalicylic acid synthase from Penicillium patulum was expressed in E. coli and S. cerevisiae and the polyketide 6-methylsalicylic acid (6-MSA) was produced. In both bacterial and yeast hosts, polyketide production required coexpression of 6-methylsalicylic acid synthase and a heterologous phosphopantetheinyl transferase that was required to convert the expressed apo-PKS to its holo form. Production of 6-MSA in E. coli was both temperature- and glycerol-dependent and levels of production were lower than those of P. patulum, the native host. In yeast, however, 6-MSA levels greater than 2-fold higher than the native host were observed. The heterologous expression systems described will facilitate the manipulation of PKS genes and consequent production of novel engineered polyketides and polyketide libraries.
The Bacillus subtilis enzyme Sfp, required for production of the lipoheptapeptide antibiotic surfactin, posttranslationally phosphopantetheinylates a serine residue in each of the seven peptidyl carrier protein domains of the first three subunits (SrfABC) of surfactin synthetase to yield docking sites for amino acid loading and peptide bond formation. With recombinant Sfp and 16-17-kDa peptidyl carrier protein (PCP) domains excised from the SrfB1 and SrfB2 modules as apo substrates, kcat values of 56-104 min-1 and K(m) values of 1.3-1.8 microM were determined, indicating equivalent recognition of the adjacent PCP domains by Sfp. In contrast to other phosphopantetheinyl transferases (PPTases) previously examined, Sfp will modify the apo forms of heterologous recombinant proteins, including the PCP domain of Saccharomyces cerevisiae Lys2 (involved in lysine biosynthesis), the aryl carrier protein (ArCP) domain of Escherichia coli EntB (involved in enterobactin biosynthesis), and the E. coli acyl carrier protein (ACP) subunit, suggesting Sfp as a good candidate for heterologous coexpression with peptide and polyketide synthase genes to overproduce holo-synthase enzymes. Cosubstrate coenzyme A (CoA), the phosphopantetheinyl group donor, has a K(m) of 0.7 microM. Desulfo-CoA and homocysteamine-CoA are also substrates of Sfp, and benzoyl-CoA and phenylacetyl-CoA are also utilized by Sfp, resulting in direct transfer of acyl phosphopantetheinyl moieties into the carrier protein substrate. Mutagenesis in Sfp of five residues conserved across the PPTase family was assessed for in vivo effects on surfactin production and in vitro effects on PPTase activity.
Polyketides and non-ribosomal peptides are two large families of complex natural products that are built from simple carboxylic acid or amino acid monomers, respectively, and that have important medicinal or agrochemical properties. Despite the substantial differences between these two classes of natural products, each is synthesized biologically under the control of exceptionally large, multifunctional proteins termed polyketide synthases (PKSs) and non-ribosomal peptide synthetases (NRPSs) that contain repeated, coordinated groups of active sites called modules, in which each module is responsible for catalysis of one complete cycle of polyketide or polypeptide chain elongation and associated functional group modifications. It has recently become possible to use molecular genetic methodology to alter the number, content, and order of such modules and, in so doing, to alter rationally the structure of the resultant products. This review considers the promise and challenges inherent in the combinatorial manipulation of PKS and NRPS structure in order to generate entirely "unnatural" products.
Combinatorial biosynthesis involves interchanging secondary metabolism genes between antibiotic-producing microorganisms to create unnatural gene combinations or hybrid genes if only part of a gene is exchanged. Novel metabolites can be made by both approaches, due to the effect of a new enzyme on a metabolic pathway or to the formation of proteins with new enzymatic properties. The method has been particularly successful with polyketide synthase (PKS) genes: derivatives of medically important macrolide antibiotics and unusual polycyclic aromatic compounds have been produced by novel combinations of the type I and type II PKS genes, respectively. Recent extensions of the approach to include deoxysugar biosynthesis genes have expanded the possibilities for making new microbial metabolites and discovering valuable drugs through the genetic engineering of bacteria.
In the production of secondary metabolites yield and productivity are the most important design parameters. The focus is therefore to direct the carbon fluxes towards the product of interest, and this can be obtained through metabolic engineering whereby directed genetic changes are introduced into the production strain. In this process it is, however, important to analyze the metabolic network through measurement of the intracellular metabolites and the flux distributions. Besides playing an important role in the optimization of existing processes, metabolic engineering also offers the possibility to construct strains that produce novel metabolites, either through the recruitment of heterologous enzyme activities or through introduction of specific mutations in catalytic activities.
Polyketide synthases (PKSs) and nonribosomal peptide synthetases (NRPSs) catalyze chain elongation from simple building blocks to create a diverse array of natural products. PKS and NRPS proteins share striking architectural and organizational similarities that can be exploited to generate entirely new natural products.
Histone N-acetyltransferases (HATs) are a group of enzymes which acetylate specific lysine residues in the N-terminal tails of nucleosomal histones to promote transcriptional activation. Recent structural and enzymatic work on the GCN5/PCAF HAT family has elucidated the structure of their catalytic domain and mechanism of histone acetylation. However, the substrate specificity of these enzymes has not been quantitatively investigated. Utilizing a novel microplate fluorescent HAT assay which detects the enzymatic production of coenzyme A (CoA), we have compared the activities of the HAT domains of human PCAF and its GCN5 homologue from yeast and Tetrahymena and found that they have similar kinetic parameters. PCAF was further assayed with a series of different length histone H3 peptide substrates, which revealed that the determinants for substrate recognition lie within a 19-residue sequence. Finally, we evaluated the acetylation of three putative PCAF substrates, histones H3 and H4 and the transcription factor p53, and have determined that histone H3 is significantly preferred over the histone H4 and p53 substrates. Taken together, the fluorescent acetyltransferase assay presented here should be widely applicable to other HAT enzymes, and the results obtained with PCAF demonstrate a strong substrate preference for the N-terminal residues of histone H3.
Multicopy plasmids are often chosen for the expression of recombinant genes in Escherichia coli. The high copy number is generally desired for maximum gene expression; however, the metabolic burden effects that usually result from multiple plasmid copies could prove to be detrimental for maximum productivity in certain metabolic engineering applications. In this study, low-copy mini-F plasmids were compared to high-copy pMB1-based plasmids for production of two metabolites in E. coli: polyphosphate (polyP) and lycopene derived from isopentenyl diphosphate (IPP). The stationary-phase accumulation of polyP on a per cell basis was enhanced approximately 80% when either high- or low-copy plasmids were used, from 120 micromol/g DCW without augmented polyP kinase (PPK) activity to approximately 220 micromol/g DCW. The cell density of the high-copy plasmid-containing culture at stationary phase was approximately 24% lower than the low-copy culture and 30% lower than the control culture. This difference in cell density is likely a metabolic burden effect and resulted in a lower overall product concentration for the high-copy culture (approximately 130 micromol/L culture) relative to the low-copy culture (approximately 160 micromol/L culture). When the gene for DXP (1-deoxy-D-xylulose 5-phosphate) synthase, the first enzyme in the IPP mevalonate-independent biosynthetic pathway, was expressed from the tac promoter on multicopy and low-copy plasmids, lycopene production was enhanced two- to threefold over that found in cells expressing the chromosomal copy only. Cell growth and lycopene production decreased substantially when isopropyl beta-D-thiogalactosidase (IPTG) was added to the high-copy plasmid-containing culture, suggesting that overexpression of DXP synthase was a significant metabolic burden. In the low-copy plasmid-containing culture, no differences in cell growth or lycopene production were observed with any IPTG concentrations. When dxs was placed under the control of the arabinose-inducible promoter (P(BAD)) on the low-copy plasmid, the amount of lycopene produced was proportional to the arabinose concentration and no significant changes in cell growth resulted. These results suggest that low-copy plasmids may be useful in metabolic engineering applications, particularly when one or more of the substrates used in the recombinant pathway are required for normal cellular metabolism.
The structural and catalytic similarities between modular nonribosomal peptide synthetase (NRPS) and polyketide synthase (PKS) inspired us to search for hybrid NRPS-PKS systems. By examining the biochemical and genetic data known to date for the biosynthesis of hybrid peptide-polyketide natural products, we show (1) that the same catalytic sites are conserved between the hybrid NRPS-PKS and normal NRPS or PKS systems, although the ketoacyl synthase domain in NRPS/PKS hybrids is unique, and (2) that specific interpolypeptide linkers exist at both the C- and N-termini of the NRPS and PKS proteins, which presumably play a critical role in facilitating the transfer of the growing peptide or polyketide intermediate between NRPS and PKS modules in hybrid NRPS-PKS systems. These findings provide new insights for intermodular communications in hybrid NRPS-PKS systems and should now be taken into consideration in engineering hybrid peptide-polyketide biosynthetic pathways for making novel "unnatural" natural products.
Microbial nonribosomally processed peptides represent a large class of natural products including numerous important pharmaceutical agents, as well as other representatives that play a prevalent role in pathogenicity of certain microorganisms [M. A. Marahiel, T. Stachelhaus, and H. D. Mootz (1997). Chem. Rev. 97, 2651-2673]. Although diverse in structure, nonribosomally synthesized peptides have a common mode of biosynthesis. They are assembled on very large protein templates called peptide synthetases that exhibit a modular organization, allowing polymerization of monomers in an assembly-line-like mechanism.
Metabolic engineering of natural products is a science that has been built on the goals of traditional strain improvement with the availability of modern molecular biological technologies. In the past 15 years, the state of the art in metabolic engineering of natural products has advanced from the first proof-of-principle experiment based on minimal known genetics to a commonplace event using highly specific and sophisticated gene manipulation methods. With the availability of genes, host organisms, vector systems, and standard molecular biological tools, it is expected that metabolic engineering will be translated into industrial reality.
Polyketide natural products show great promise as medicinal agents. Typically the products of microbial secondary biosynthesis, polyketides are synthesized by an evolutionarily related but architecturally diverse family of multifunctional enzymes called polyketide synthases. A principal limitation for fundamental biochemical studies of these modular megasynthases, as well as for their applications in biotechnology, is the challenge associated with manipulating the natural microorganism that produces a polyketide of interest. To ameliorate this limitation, over the past decade several genetically amenable microbes have been developed as heterologous hosts for polyketide biosynthesis. Here we review the state of the art as well as the difficulties associated with heterologous polyketide production. In particular, we focus on two model hosts, Streptomyces coelicolor and Escherichia coli. Future directions for this relatively new but growing technological opportunity are also discussed.
The structural and catalytic similarities between non-ribosomal peptide synthetase (NRPS) and polyketide synthase (PKS) support the idea of combining individual NRPS and PKS modules for combinatorial biosynthesis. Recent advances in cloning and characterization of biosynthetic gene clusters for naturally occurring hybrid polyketide-peptide metabolites have provided direct evidence for the existence of hybrid NRPS-PKS systems, thus setting the stage to investigate the molecular basis for intermodular communication between NRPS and PKS modules. Reviewed in this article are biosynthetic data pertinent to hybrid peptide-polyketide biosynthesis published up to late 2000. Hybrid peptide-polyketide natural products can be divided into two classes: (i) those whose biosyntheses do not involve functional interaction between NRPS and PKS modules; and (ii) those whose biosyntheses are catalyzed by hybrid NRPS-PKS systems involving direct interactions between NRPS and PKS modules. It is the latter systems that are most likely amenable to combinatorial biosynthesis. The same catalytic sites appear to be conserved in both hybrid NRPS-PKS and normal NRPS or PKS systems, with the exception of the ketoacyl synthase domains in hybrid NRPS-PKS systems which are unique. Specific linkers may play a critical role in communication, facilitating the transfer of the growing intermediates between the interacting NRPS and/or PKS modules. In addition, phosphopantetheinyl transferases with broad carrier protein specificity are essential for the production of functional hybrid NRPS-PKS megasynthetases. These findings should now be taken into consideration in engineered biosynthesis of hybrid peptide-polyketide natural products for drug discovery and development.
After washing, the samples were boiled in 50 l 1ϫ SDS sample buffer for 10 min and centrifuged, and the superna A new enzyme superfamily—the phosphopantetheinyl trans-tant run on a 12% Tris-Glycine SDS-PAGE gel and analyzed by Western blot. For 2f
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Derivatizations of agarose and polyacrylamide beads
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