Biochemical Characterization of the C4-Dicarboxylate Transporter DctA from Bacillus subtilis

Bacterial secondary transporters of the DctA family mediate ion-coupled uptake of C₄-dicarboxylates. Here, we have expressed the DctA homologue from Bacillus subtilis in the Gram-positive bacterium Lactococcus lactis. Transport of dicarboxylates in vitro in isolated membrane vesicles was assayed. We determined the substrate specificity, the type of cotransported ions, the electrogenic nature of transport, and the pH and temperature dependence patterns. DctA was found to catalyze proton-coupled symport of the four C₄-dicarboxylates from the Krebs cycle (succinate, fumurate, malate, and oxaloacetate) but not of other mono- and dicarboxylates. Because (i) succinate-proton symport was electrogenic (stimulated by an internal negative membrane potential) and (ii) the divalent anionic form of succinate was recognized by DctA, at least three protons must be cotransported with succinate. The results were interpreted in the light of the crystal structure of the homologous aspartate transporter Glt_Ph from Pyrococcus horikoshii.The DctA family is one of several diverse families of secondary transporters that catalyze the uptake of C₄-dicarboxylates from the Krebs cycle in bacteria (16, 27). In Escherichia coli, DctA mediates the uptake of succinate, fumurate, and malate under aerobic conditions; genomic disruption of dctA in E. coli prevents growth with malate or fumarate as the sole carbon source, and the mutant grows poorly on succinate (5). Similarly, a dctA knockout mutant of Bacillus subtilis cannot grow with succinate or fumarate as the sole carbon source (1). DctA plays a major role in the symbiotic relationship between nitrogen-fixing rhizobia (43) and root nodule-forming plants (30, 37, 38). Transport assays with Sinorhizobium meliloti cells showed previously that in addition to succinate, malate, and fumarate, orotate is transported and that a range of other substrates such as succinamic acid and succinamide may be transported, because they inhibit the transport of orotate (42). In Corynebacterium glutamicum, malate transport by DctA is inhibited by α-ketoglutarate, oxaloacetate, and glyoxylate, indicating that these compounds may be substrates also (41).DctA transporters belong to a large family of secondary transporters (the DAACS [dicarboxylate/amino acid:cation symporter] family), which also comprises well-characterized glutamate/aspartate transporters and neutral amino acid transporters (32, 33). While DctA-type dicarboxylate transporters are found only in bacteria, glutamate/aspartate transporters of the DAACS family are found both in prokaryotes (e.g., GltT in Bacillus stearothermophilus, GltP in E. coli, and Glt_Ph in Pyrococcus horikoshii [2, 7, 34]) and in higher eukarya, where they play a pivotal role in the reuptake of the excitatory neurotransmitter glutamate from the synaptic cleft (4). Neutral amino acid (alanine, serine, and threonine) transporters are found in mammals (see, e.g., references 36 and 44) as well as bacteria (17).Secondary transporters of the DAACS family use (electro)chemical gradients of cations across the membrane to drive transport. The type of cotransported ions varies among family members: eukaryotic glutamate transporters couple the transport of glutamate to the symport of one proton and three sodium ions and the antiport of one potassium ion (24, 45). Bacterial and archaeal glutamate transporters utilize either sodium ions or protons for symport (2) and are independent of potassium ions (28, 31). The bacterial and mammalian neutral amino acid transporters are sodium ion coupled. Glutamate/aspartate transporters and bacterial serine/threonine transporters (SstTs) are electrogenic, but mammalian neutral amino acid transporters are obligate electroneutral amino acid antiporters (44).Insight into the structure-function relationships of the DAACS family members has greatly increased since crystal structures of the P. horikoshii aspartate transporter Glt_Ph have been determined (2, 29, 40). The protein consists of eight membrane-spanning helices and two reentrant regions (helical hairpins HP1 and HP2) (40). The C-terminal part of the protein (helices 7 and 8 and HP1 and HP2) is most strongly conserved with respect to other family members and binds the substrate and cotransported ions, with HP1 and HP2 functioning as lids that allow alternating access to the substrate- and ion-binding sites from either side of the membrane (3, 29). Glt_Ph forms a homotrimeric complex in which each protomer functions independently of the other subunits (11, 12, 18, 19, 23). The fold and oligomeric state are likely to be conserved throughout the family.Whereas the transport mechanisms of bacterial glutamate and neutral amino acid transporters of the DAACS family have been studied extensively in vitro, the C₄-dicarboxylate transporters of the DAACS family (DctA proteins) have been studied using whole cells only. To fully characterize these transporters, in vitro activity assays using either membrane vesicles or proteoliposomes containing purified protein are necessary. In such assays, the internal and external buffer compositions can be controlled, thus allowing manipulation of the chemical ion gradients and the electrical potential across the membrane. Here, we present the first biochemical characterization of a DctA family member in membrane vesicles. We have studied the DctA homologue from B. subtilis, which is annotated as DctP (1) but which we propose to rename DctA to reflect the homology to other DctA proteins. B. subtilis DctA (DctA_Bs) has 30 to 32% sequence identity to the aspartate transporter Glt_Ph and human excitatory amino acid transporter (EAAT) family members, over 40% sequence identity to the characterized bacterial glutamate transporters from E. coli and B. stearothermophilus, and 41 and 56% identity to DctA homologues from C. glutamicum and E. coli, respectively. We determined the substrate specificity of DctA_Bs, the type of cotransported ions, the electrogenic nature of transport, and the pH and temperature dependence patterns.     

Isolation and Characterization of a Novel Lysine Racemase from a Soil Metagenomic Library

A lysine racemase (lyr) gene was isolated from a soil metagenome by functional complementation for the first time by using Escherichia coli BCRC 51734 cells as the host and d-lysine as the selection agent. The lyr gene consisted of a 1,182-bp nucleotide sequence encoding a protein of 393 amino acids with a molecular mass of about 42.7 kDa. The enzyme exhibited higher specific activity toward lysine in the l-lysine-to-d-lysine direction than in the reverse reaction.Amino acids are the building blocks of proteins and play an important role in the regulation of the metabolism of living organisms. Among two enantiomers of naturally occurring amino acids, l-amino acids are predominant in living organisms, while d-amino acids are found in both free and bound states in various organisms like bacteria (36), yeasts (35), plants (47), insects (11), mammals (17), bivalves (39), and fish (28). The d-amino acids are mostly endogenous and produced by racemization from their counterparts by the action of a racemase. Thus, the amino acid racemases are involved in d-amino acid metabolism (29, 46). Since the discovery of alanine racemase in 1951 (42), several racemases toward amino acids, such as those for glutamate, threonine, serine, aspartate, methionine, proline, arginine, and phenylalanine, have been reported in bacteria, archaea, and eukaryotes, including mammals (1, 2, 15, 30, 31, 44). They are classified into two groups: pyridoxal 5′-phosphate (PLP)-dependent and PLP-independent enzymes (9, 36).Lysine racemase (Lyr, EC 5.1.1.5) was first reported in Proteus vulgaris ATCC 4669 (19) and proposed to be involved in the lysine degradation of bacterial cells (5, 19). Catabolism of lysine occurs via two parallel pathways. In one of the pathways, δ-aminovalerate is the key metabolite, whereas in the other l-lysine is racemized to d-lysine, and l-pipecolate and α-aminoadipate (AMA) are the key metabolites (5). d-Lysine catabolism proceeds through a series of cyclized intermediates which are necessary to regenerate an α-amino acid and comprise the following metabolites (AMA pathway): d-lysine→α-keto-ɛ-amino caproate→Δ¹-piperideine-2-carboxylate→pipecolate→Δ¹-piperideine-6-carboxylate→α-amino-δ-formylcaproate→α-AMA→α-ketoadipate (6, 7, 12, 27). The final product is converted to α-ketoglutarate via a series of coenzyme A derivatives and subsequently participates as an intermediate in the Krebs cycle. This pathway suggests that the biological function of d-lysine in the bacteria is that of a carbon or nitrogen source. Racemization of added l-lysine to d-lysine by whole cells of Proteus spp. and Escherichia spp. (19) and by the cell extract of Pseudomonas putida ATCC 15070 (5, 20) has been found. However, the enzyme has not been purified to homogeneity, and thus, its molecular and catalytic characteristics, including its gene structure, have not been elucidated. In this study, we explored a metagenomic library constructed from a garden soil to isolate a novel Lyr enzyme. After expression in Escherichia coli, the purified enzyme was characterized in terms of optimal pH and temperature, thermal stability, and racemization activity.     

Requirements for Germination of Clostridium sordellii Spores In Vitro

Clostridium sordellii is a spore-forming, obligately anaerobic, Gram-positive bacterium that can cause toxic shock syndrome after gynecological procedures. Although the incidence of C. sordellii infection is low, it is fatal in most cases. Since spore germination is believed to be the first step in the establishment of Bacilli and Clostridia infections, we analyzed the requirements for C. sordellii spore germination in vitro. Our data showed that C. sordellii spores require three structurally different amino acids and bicarbonate for maximum germination. Unlike the case for Bacilli species, d-alanine had no effect on C. sordellii spore germination. C. sordellii spores germinated only in a narrow pH range between 5.7 and 6.5. In contrast, C. sordellii spore germination was significantly less sensitive to temperature changes than that of the Bacilli. The analysis of the kinetics of C. sordellii spore germination showed strong allosteric behavior in the binding of l-phenylalanine and l-alanine but not in that of bicarbonate or l-arginine. By comparing germinant apparent binding affinities to their known in vivo concentrations, we postulated a mechanism for differential C. sordellii spore activation in the female reproductive tract.Clostridium sordellii is an anaerobic, Gram-positive, spore-forming bacterium that is commonly found in soil and in the intestines of animals (4). Many C. sordellii strains are nonpathogenic; however, virulent strains cause lethal infections in several animal species, such as hemorrhagic enteritis in foals, sheep, and cattle (5, 10, 16, 28), omphalitis in foals (43), and wound infection in humans (4, 35).C. sordellii also can cause life-threatening necrotizing infections after gynecological procedures (4). In addition, fatal cases of C. sordellii endometritis following medical abortion with a mifepristone-misoprostol combination have been reported recently (13, 19, 56). The increased use of mifepristone-misoprostol for medical abortion may result in larger numbers of C. sordellii infections (38, 40).Although C. sordellii rarely has been identified in the genital tract, a correlation between gynecological procedures and C. sordellii-mediated toxic shock syndrome is apparent (19). Pregnancy, childbirth, or abortion may predispose some women to acquire C. sordellii in the vaginal tract (19). Under these conditions, C. sordellii infections result in an almost 100% mortality rate.Since there is no national system for tracking and reporting complications associated with gynecological procedures, the identification of the true rates of reproductive tract infections in women is not readily available (8). Therefore, the number of known C. sordellii-associated infections, although low, may be underreported (19, 29). Furthermore, unsafe abortion practices in developing countries cause large mortality rates due to complicating infections (24, 34). In many cases, however, the causative agent of the abortion-associated sepsis have not been characterized (24). Thus, the worldwide morbidity and mortality associated with C. sordellii infections is not currently known.C. sordellii produces several virulence factors. The two major toxins are the lethal toxin (TcsL) and the hemorrhagic toxin (37, 46). The lethal toxin produced by C. sordellii is causally involved in enteritis of domestic animals and in systemic toxicity following infections of humans (46). Furthermore, TcsL is associated with rapid mortality in C. sordellii endometritis rodent models (26). Interestingly, TcsL cytopathic effects are increased at low pH, a characteristic found in the vaginal tract (48). The hemorrhagic toxin is not well characterized, but it has been reported to cause dermal and intestinal necrosis in guinea pigs (6, 52).C. sordellii, like other Bacilli and Clostridia species, has the ability to form metabolically dormant spores that are extremely resistant to environmental stresses, such as heat, radiation, and toxic chemicals (42, 55). Upon encountering a suitable environment, spores germinate into vegetative cells, the form that is responsible for toxin production and disease onset (39, 54).In most cases, the germination process initially is triggered by the detection of low-molecular-weight germinants by a sensitive biosensor (39, 54). This sensor consists of a proteinaceous germination (Ger) receptor encoded, in general, by a tricistronic operon. Spore germination requirements have been studied most extensively for Bacilli and can be initiated by a variety of factors, including amino acids, sugars, and nucleosides (20, 30).Spore germination in the Clostridia generally requires combinations of multiple germinants. The germination of spores of proteolytic Clostridium botulinum types A and B was triggered by a defined three-component mixture comprised of l-alanine (or l-cysteine), l-lactate (or sodium thioglycolate), and sodium bicarbonate (3). In contrast, the optimum germination of spores of nonproteolytic C. botulinum types B, E, and F required binary combinations of l-alanine-l-lactate, l-cysteine-l-lactate, and l-serine-l-lactate (45).Clostridium difficile is a human pathogen that can cause fulminant colitis (11). Interestingly, C. difficile does not encode any known Ger receptors (53). However, it is likely that germination receptors exist, because C. difficile spores must germinate in order to complete their life cycle. While C. difficile germination receptors remain elusive, the spores of C. difficile germinate in rich medium supplemented with bile salts (62). More recently, taurocholate (a bile salt) and glycine (an amino acid) were shown to act as cogerminants for C. difficile spore germination (57, 61).Clostridium bifermentans is a close relative of C. sordellii (14). The minimum requirement for C. bifermentans spore germination was the presence of l-alanine, l-phenylalanine, and l-lactate (59). In addition, an unknown factor present in yeast extract was suggested to enhance germination (59). However, the Ger receptors involved in C. bifermentans spore germination are not known.Even though many Bacilli and Clostridia species use similar metabolites as germinants, the mechanisms of germinant recognition remain to be elucidated. Unfortunately, the multimeric interactions of Ger receptor complexes and the hydrophobic nature of the Ger receptor subunits have hindered our understanding of the mechanism of germinant recognition.To understand the molecular determinants of germinant recognition, we recently applied kinetic methods to study bacterial spore germination (1, 2, 18). Spore germination can be analyzed quantitatively by fitting optical density (OD) decreases to the Michaelis-Menten equation (2). The kinetic parameters obtained allow the determination of the apparent binding affinity (K_m) of spores for the different cogerminants and the maximum rate of spore germination (V_max). In these instances, K_m refers to the concentration of substrate required to reach half of the maximal germination rate. These parameters can, in turn, be used to determine the mechanism of germination and potential interactions between germination receptors. Furthermore, by comparing apparent K_m values to germinant concentrations in vivo, models for spore-germinant complex distribution can be proposed, and rate-limiting steps for the germination process can be derived. Thus, kinetic analysis can yield information on spore activation even if the identities of the germination receptors are not known.Using this procedure, we were able to determine the mechanism for Bacillus anthracis germination with inosine and l-alanine. In turn, this information was used to design nucleoside analogs that inhibit B. anthracis spore germination in vitro and protect macrophages from anthrax cytotoxicity (2).Since C. sordellii germination receptors have not been identified, we used chemical probes and kinetic methods to investigate the conditions necessary for spore germination. We found that C. sordellii spores germinate better at slightly acidic pH. Furthermore, germination rates varied slightly from 25 to 40°C. We also found that C. sordellii spores have an absolute requirement for a small amino acid, a basic amino acid, an aromatic amino acid, and bicarbonate (NaHCO₃) for efficient germination. Kinetic analysis showed allosteric interaction for the putative l-phenylalanine and l-alanine germination receptors. In contrast, l-arginine or bicarbonate recognition followed typical Michaelis-Menten kinetics. The implication of germinant recognition and host environment is discussed.     

Exopolyphosphatases PPX1 and PPX2 from Corynebacterium glutamicum

Corynebacterium glutamicum accumulates up to 300 mM of inorganic polyphosphate (PolyP) in the cytosol or in granules. The gene products of cg0488 (ppx1) and cg1115 (ppx2) were shown to be active as exopolyphosphatases (PPX), as overexpression of either gene resulted in higher exopolyphosphatase activities in crude extracts and deletion of either gene with lower activities than those of the wild-type strain. PPX1 and PPX2 from C. glutamicum share only 25% identical amino acids and belong to different protein groups, which are distinct from enterobacterial, archaeal, and yeast exopolyphosphatases. In comparison to that in the wild type, more intracellular PolyP accumulated in the Δppx1 and Δppx2 deletion mutations but less when either ppx1 or ppx2 was overexpressed. When C. glutamicum was shifted from phosphate-rich to phosphate-limiting conditions, a growth advantage of the deletion mutants and a growth disadvantage of the overexpression strains compared to the wild type were observed. Growth experiments, exopolyphosphatase activities, and intracellular PolyP concentrations revealed PPX2 as being a major exopolyphosphatase from C. glutamicum. PPX2^His was purified to homogeneity and shown to be active as a monomer. The enzyme required Mg²⁺ or Mn²⁺ cations but was inhibited by millimolar concentrations of Mg²⁺, Mn²⁺, and Ca²⁺. PPX2 from C. glutamicum was active with short-chain polyphosphates, even accepting pyrophosphate, and was inhibited by nucleoside triphosphates.Inorganic polyphosphate (PolyP), a linear polymer made of up to hundreds of orthophosphate residues (P_i), has been found in all organisms tested for its presence (3, 4, 7, 12, 20, 22, 48). In nature''s phosphorus cycle, diatom-derived PolyP has recently been shown to be critically important for marine phosphorus sequestration (6). In cells, PolyP may function as a means of storage of phosphorus and/or energy, may substitute ATP in kinase reactions, and was shown to be important in response to many stresses. Mutants of Escherichia coli, Pseudomonas aeruginosa, Shigella spp., Salmonella spp., Vibrio cholerae, and Helicobacter pylori with a low PolyP content showed defects in environmental stress responses and/or virulence (2, 14, 17, 38). In amino acid-starved E. coli, PolyP accumulates and is bound by Lon protease, which degrades ribosomal proteins to liberate amino acids (23).The presence of PolyP granules is used as a diagnostic criterion to distinguish the pathogenic Corynebacterium diphtheriae from nonpathogenic corynebacteria, such as Corynebacterium glutamicum (54). However, these metachromatic granules have recently been shown to be present also in nonpathogenic C. glutamicum (33). When sufficient phosphate is available, C. glutamicum accumulates up to 300 mM of PolyP (24) either soluble in the cytosol or in volutin granules (18, 33). During growth of C. glutamicum on glucose, intracellular PolyP concentrations peaked in the early exponential growth phase and at the entry to stationary phase (18). Soluble PolyP prevailed in the stationary growth phase, while PolyP occurred in granules in the early exponential growth phase (18). C. glutamicum is widely used for the biotechnological production of about 2,200,000 tons of amino acids per year, mainly l-glutamate and l-lysine (50, 58), while the related Corynebacterium ammoniagenes is used for the production of the flavor-enhancing purine nucleotides IMP and XMP (30). As it is conceivable that engineering corynebacterial PolyP metabolism affects overproduction of amino acids or of the phosphorus-containing compounds IMP and XMP, the study of PolyP metabolism and the enzymes involved has recently received increasing attention.PolyP formation in C. glutamicum was shown to be stimulated by MgCl₂ (33), probably due to the magnesium dependence of PolyP synthesizing enzymes (27). In microorganisms, PolyP may be synthesized by PolyP kinases belonging to three distinct families (PPK1, PPK2, and PPK3; EC 2.7.4.1) from ATP or other nucleoside triphosphates (NTPs) in a reversible reaction (12). C. glutamicum possesses two PPK2 genes (ppk2A and ppk2B) (27). Purified PPK2B of C. glutamicum is active as a homotetramer and shows higher catalytic efficiency in the PolyP-forming direction than in the reverse direction, forming NTPs from PolyP. The intracellular PolyP content was increased by overexpression of ppk2B and decreased in the absence of PPK2B (27). Besides PPK2B, no other PolyP-dependent enzyme has been characterized in C. glutamicum, although the cg2091 gene product, a putative PolyP-dependent glucokinase (EC 2.7.1.63), was found to be associated with PolyP granules (33).Degradation of PolyP by hydrolysis may be catalyzed by exopolyphosphatases (PPX) (EC 3.6.1.11) and/or endopolyphosphatases (PPN) (EC 3.6.1.10) (1, 49). Exopolyphosphatases hydrolyze PolyP from the chain''s termini, liberating P_i. The C. glutamicum genome contains two genes encoding putative exopolyphosphatases (ppx1-cg0488 and ppx2-cg1115) (15), but their functions have not yet been characterized. The corresponding proteins are distinct from each other as they share only 25% identical amino acids. Both proteins show 25% amino acid identity to E. coli PPX (1), which possesses 200 additional C-terminal amino acids (56). Here, we have analyzed PolyP degradation in C. glutamicum and show that both cg0488 (ppx1) and cg1115 (ppx2) gene products are functional exopolyphosphatases. Growth experiments, determination of exopolyphosphatase activities, and intracellular PolyP concentrations in strains lacking or overexpressing these genes revealed that cg1115 (ppx2) encodes the major exopolyphosphatase of C. glutamicum, which was characterized enzymatically.     

The Aminolysis Reaction of Streptomyces S9 Aminopeptidase Promotes the Synthesis of Diverse Prolyl Dipeptides

Prolyl dipeptide synthesis by S9 aminopeptidase from Streptomyces thermocyaneoviolaceus (S9AP-St) has been demonstrated. In the synthesis, S9AP-St preferentially used l-Pro-OBzl as the acyl donor, yielding synthesized dipeptides having an l-Pro-Xaa structure. In addition, S9AP-St showed broad specificity toward the acyl acceptor. Furthermore, S9AP-St produced cyclo (l-Pro-l-His) with a conversion ratio of substrate to cyclo (l-Pro-l-His) higher than 40%.Some proline-containing dipeptides and their cyclic analogs exhibit biological activity. For example, cyclo (l-arginyl-d-proline) [c(lR-dP)] is known to act as a specific inhibitor of family 18 chitinase (4, 10). A cyclic peptide, c(lP-lH), produced by the cleavage of thyrotropin-releasing hormone protects against oxidative stress, promotes cytoprotection (6, 7), and exhibits antihyperglycemic activity (11).Some serine peptidases exhibit peptide bond formation (i.e., aminolysis of esters, thioesters, and amides) in accordance with their hydrolytic activity (2, 14). The exchange of catalytic Ser for Cys to engineer the serine endopeptidase into “transpeptidase” for peptide bond formation has been well characterized (3, 5). Our recent approach confirmed the wide distribution of family S9 aminopeptidases that have catalytic Ser in actinomycetes (12). Of them, we obtained S9 aminopeptidase from Streptomyces thermocyaneoviolaceus NBRC14271 (S9AP-St). The enzyme was engineered into “transaminopeptidase” by exchange of catalytic Ser for Cys, and its aminolytic activity was evaluated (13). The engineered enzyme, designated as aminolysin-S, can synthesize hydrophobic dipeptides through an aminolysis reaction. However, aminolysin-S was unable to synthesize peptides containing proline. Although the report of aminolysin-S demonstrated that S9AP-St shows no aminolysis reaction toward limited substrates, details of its characteristics remain unknown. This study verified the peptide synthetic activity of S9AP-St, demonstrating that S9AP-St can synthesize widely varied prolyl dipeptides through an aminolysis reaction. The report also shows that S9AP-St is applicable to the synthesis of a biologically active peptide—c(lP-lH).     

Identification and Characterization of gshA,a Gene Encoding the Glutamate-Cysteine Ligase in the Halophilic Archaeon Haloferax volcanii

Halophilic archaea were found to contain in their cytoplasm millimolar concentrations of γ-glutamylcysteine (γGC) instead of glutathione. Previous analysis of the genome sequence of the archaeon Halobacterium sp. strain NRC-1 has indicated the presence of a sequence homologous to sequences known to encode the glutamate-cysteine ligase GshA. We report here the identification of the gshA gene in the extremely halophilic archaeon Haloferax volcanii and show that H. volcanii gshA directs in vivo the synthesis and accumulation of γGC. We also show that the H. volcanii gene when expressed in an Escherichia coli strain lacking functional GshA is able to restore synthesis of glutathione.Many organisms contain millimolar concentrations of low-molecular-weight thiol compounds that participate in a number of important biological functions involving thiol-disulfide exchanges (7). In particular, they serve to maintain an intracellular reducing environment, to provide reducing power for key reductive enzymes, to combat the effects of oxidative and disulfide stress, and to detoxify xenobiotic compounds (7). Glutathione (GSH), a cysteine-containing tripeptide, l-γ-glutamyl-l-cysteinylglycine, is the best-characterized low-molecular-weight thiol (7, 19, 21). GSH is made in a highly conserved two-step ATP-dependent process by two unrelated peptide bond-forming enzymes (3, 21). The γ-carboxyl group of l-glutamate and the amino group of l-cysteine are ligated by the enzyme glutamylcysteine (GC) ligase EC 6.3.2.2 (GshA, encoded by gshA), which is then condensed with glycine in a reaction catalyzed by GSH synthetase (GshB, encoded by gshB) to form GSH (10, 38). GSH is found primarily in gram-negative bacteria and eukaryotes and only rarely in gram-positive bacteria (26). Fahey and coworkers showed that GSH is absent from the high-GC gram-positive actinomycetes which produce, as the major low-molecular-weight thiol, mycothiol, 1-d-myo-inosityl-2-(N-acetyl-l-cysteinyl)-amido-2-deoxy-α-d-glucopyranoside (13, 26-28, 35). GSH is also absent in Archaea. In Pyrococcus furiosus, coenzyme A SH (CoASH) is the main thiol (11), whereas in Halobacterium salinarum, γGC is the predominant thiol and the organism possesses bis-γGC reductase activity (30, 36). Similarly, Leuconostoc kimchi and Leuconostoc mesenteroides, gram-positive lactic acid bacterial species, were recently found to contain γGC rather than GSH (15). To date, these are the sole procaryotic species reported to naturally produce γGC but not GSH (6, 30). In this report, we describe the identification of the gshA gene in the extremely halophilic archaeon Haloferax volcanii. Copley and Dhillon (6) previously identified, using bioinformatic tools, an open reading frame (ORF) (gene VNG1397C) in Halobacterium sp. strain NRC-1 with limited sequence relatedness to known GshA proteins (6). However, no genetic or biochemical evidence was presented to substantiate their conclusion. Here, we show that Haloferax volcanii strain DS2 (1, 25) contains an ORF that directs in vivo the synthesis and accumulation of γGC. We also show that the H. volcanii ORF, when expressed in Escherichia coli lacking functional GshA, is able to restore synthesis of GSH.     

Zif,the Zoocin A Immunity Factor,Is a FemABX-Like Immunity Protein with a Novel Mode of Action

Producer cell immunity to the streptococcolytic enzyme zoocin A, which is a d-alanyl-l-alanine endopeptidase, is due to Zif, the zoocin A immunity factor. Zif has high degrees of similarity to MurM and MurN (members of the FemABX family of proteins), which are responsible for the addition of amino acids to cross bridges during peptidoglycan synthesis in streptococci. In this study, purified peptidoglycans from strains with and without zif were compared to determine how Zif modifies the peptidoglycan layer to cause resistance to zoocin A. The peptidoglycan from each strain was hydrolyzed using the streptococcolytic phage lysin B30, and the resulting muropeptides were separated by reverse-phase high-pressure liquid chromatography, labeled with 4-sulfophenyl isothiocyanate, and analyzed by tandem mass spectrometry in the negative-ion mode. It was determined that Zif alters the peptidoglycan by increasing the proportion of cross bridges containing three l-alanines instead of two. This modification decreased binding of the recombinant target recognition domain of zoocin A to peptidoglycan. Zif-modified peptidoglycan also was less susceptible to hydrolysis by the recombinant catalytic domain of zoocin A. Thus, Zif is a novel FemABX-like immunity factor because it provides resistance to a bacteriolytic endopeptidase by lengthening the peptidoglycan cross bridge rather than by causing an amino acid substitution.During streptococcal peptidoglycan synthesis, monomer subunits are generated inside the cell, with nonribosomal peptidyl transferases responsible for the addition of amino acids onto the epsilon amino group of lysine in the subunits. These nonribosomal peptidyl transferases are part of the FemABX family of proteins, some of which have been implicated in penicillin resistance (5, 26). In Streptococcus pneumoniae peptidoglycan synthesis, MurM attaches either an l-alanine or an l-serine to the epsilon amino group of lysine, and MurN then adds an l-alanine (11, 26).Zoocin A is a d-alanyl-l-alanine endopeptidase produced by Streptococcus equi subsp. zooepidemicus 4881 that hydrolyzes peptidoglycan cross bridges of susceptible streptococci (12). Zoocin A has two functional domains (18). The N-terminal catalytic domain (CAT) has high degrees of similarity to several other bacteriolytic endopeptidases, including the staphylolytic enzyme lysostaphin. The C-terminal target recognition domain (TRD), which facilitates binding of the enzyme to peptidoglycan (1), has very little similarity to any characterized conserved domain.Producer cell immunity to zoocin A is due to zif (zoocin A immunity factor), which is adjacent to zooA on the chromosome and is transcribed divergently (4). Zif has high degrees of similarity to MurM and MurN and also to the lysostaphin resistance protein and other FemABX-like immunity proteins (23). Previously characterized FemABX-like immunity proteins provide resistance to peptidoglycan cross-bridge hydrolases by inserting an amino acid different from those specified by the normal FemABX-like proteins (6, 9, 15, 25), whereas Zif does not (4). It has been shown previously that Zif-specified resistance to zoocin A is an intrinsic characteristic of the peptidoglycan layer (12). Therefore, Zif must modify the peptidoglycan layer in a novel way that provides resistance to zoocin A. In the present study, Zif was shown to insert an additional l-alanine into the peptidoglycan cross bridges, which inhibited both binding of the zoocin A TRD and the ability of the zoocin A CAT to hydrolyze the cross bridge.     

Studies of the Commitment Step in the Germination of Spores of Bacillus Species

Spores of Bacillus species are said to be committed when they continue through nutrient germination even when germinants are removed or their binding to spores'' nutrient germinant receptors (GRs) is both reversed and inhibited. Measurement of commitment and the subsequent release of dipicolinic acid (DPA) during nutrient germination of spores of Bacillus cereus and Bacillus subtilis showed that heat activation, increased nutrient germinant concentrations, and higher average levels of GRs/spore significantly decreased the times needed for commitment, as well as lag times between commitment and DPA release. These lag times were also decreased dramatically by the action of one of the spores'' two redundant cortex lytic enzymes (CLEs), CwlJ, but not by the other CLE, SleB, and CwlJ action did not affect the timing of commitment. The timing of commitment and the lag time between commitment and DPA release were also dependent on the specific GR activated to cause spore germination. For spore populations, the lag times between commitment and DPA release were increased significantly in spores that germinated late compared to those that germinated early, and individual spores that germinated late may have had lower appropriate GR levels/spore than spores that germinated early. These findings together provide new insight into the commitment step in spore germination and suggest several factors that may contribute to the large heterogeneity among the timings of various events in the germination of individual spores in spore populations.Spores of Bacillus species can remain dormant for long times and are extremely resistant to a variety of environmental stresses (26). However, under appropriate conditions, normally upon the binding of specific nutrients to spores'' nutrient germinant receptors (GRs), spores can come back to active growth through a process called germination followed by outgrowth (19, 20, 25, 26). Germination of Bacillus subtilis spores can be triggered by l-alanine or l-valine or a combination of l-asparagine, d-glucose, d-fructose, and K⁺ (AGFK). These nutrient germinants trigger germination by binding to and interacting with GRs that have been localized to the spore''s inner membrane (12, 20). l-Alanine and l-valine bind to the GerA GR, while the AGFK mixture triggers germination by interacting with both the GerB and GerK GRs (25). Normally, l-asparagine alone does not trigger B. subtilis spore germination. However, a mutant form of the GerB GR, termed GerB*, displays altered germinant specificity such that l-asparagine alone will trigger the germination of gerB* mutant spores (1, 18).A number of events occur in a defined sequence during spore germination. Initially, exposure of spores to nutrient germinants causes a reaction that commits spores to germinate, even if the germinant is removed or displaced from its cognate GR (7, 10, 21, 27, 28). This commitment step is followed by release of monovalent cations, as well as the spore core''s large pool of pyridine-2,6-dicarboxylic acid (dipicolinic acid [DPA]) along with divalent cations, predominantly Ca²⁺, that are chelated with DPA (Ca-DPA). In Bacillus spores, the release of Ca-DPA triggers the hydrolysis of spores'' peptidoglycan cortex by either of two cortex lytic enzymes (CLEs), CwlJ and SleB (11, 16, 23). CwlJ is activated during germination by Ca-DPA as it is being released from individual spores, while SleB activation requires that most Ca-DPA be released (14, 16, 17). Cortex hydrolysis, in turn, allows the spore core to expand and fully hydrate, which leads to activation of enzymes and initiation of metabolism in the spore core (21, 25).As noted above, commitment is the first event that can be assessed during spore germination, although the precise mechanism of commitment is not known. Since much has been learned about proteins important in spore germination in the many years since commitment was last studied (25, 26), it seemed worth reexamining commitment, with the goal of determining those factors that influence this step in the germination process. Knowledge of factors important in determining kinetics of commitment could then lead to an understanding of what is involved in this reaction.Kinetic analysis of spore germination, as well as commitment, has mostly been based on the decrease in optical density at 600 nm (OD₆₀₀) of spore suspensions, which monitors a combination of events that occur well after commitment, including DPA release, cortex hydrolysis, and core swelling (25-27). In the current work, we have used a germination assay that measures DPA release, an early event in spore germination, and have automated this assay to allow routine measurement of commitment, as well as DPA release from large numbers of spore samples simultaneously. This assay has allowed comparison of the kinetics of DPA release and commitment during germination and study of the effects of heat activation, germinant concentration, GR levels, and CLEs on commitment.     

Reengineering Escherichia coli for Succinate Production in Mineral Salts Medium

The fermentative metabolism of glucose was redirected to succinate as the primary product without mutating any genes encoding the native mixed-acid fermentation pathway or redox reactions. Two changes in peripheral pathways were together found to increase succinate yield fivefold: (i) increased expression of phosphoenolpyruvate carboxykinase and (ii) inactivation of the glucose phosphoenolpyruvate-dependent phosphotransferase system. These two changes increased net ATP production, increased the pool of phosphoenolpyruvate available for carboxylation, and increased succinate production. Modest further improvements in succinate yield were made by inactivating the pflB gene, encoding pyruvate formate lyase, resulting in an Escherichia coli pathway that is functionally similar to the native pathway in Actinobacillus succinogenes and other succinate-producing rumen bacteria.Succinic acid is used as a specialty chemical in the agricultural, food, and pharmaceutical industries (17, 32). It has also been identified by the U.S. Department of Energy as one of the top 12 building block chemicals (30), because it can be converted into a variety of products, including green solvents, pharmaceutical products, and biodegradable plastics (17, 32). Although succinic acid is currently produced from petroleum-derived maleic anhydride, considerable interest in the fermentative production of succinate from sugars has emerged during the past decade (9, 10, 17).Several natural succinate-producing rumen bacteria that have high rates of succinate production and high succinate yields, such as Anaerobiospirillum succiniciproducens (22), Actinobacillus succinogenes (13, 28), and “Mannheimia succiniciproducens” (15, 16), have been isolated. However, these strains require complex organic nutrients that increase the costs associated with production, purification, and waste disposal (15, 22, 28). Low levels of succinate are produced by native strains of Escherichia coli in complex and mineral salts media (1, 4). Most mutant strains of E. coli that have been described previously as succinate producers also require complex organic nutrients (18, 23-26, 29, 31). Many involve two-step aerobic and anaerobic processes (3, 23-25, 29) and the addition of foreign genes (5, 6, 23-26, 29, 31).Novel E. coli biocatalysts (KJ060, KJ071, and KJ073) for the anaerobic production of succinate in mineral salts medium have been developed recently without the use of foreign genes or resident plasmids (9, 10). These biocatalysts were developed by combining constructed mutations to eliminate alternative routes of NADH oxidation in the mixed-acid pathway with growth-based selection (metabolic evolution). In subsequent studies (33), these strains were found to have recruited the glucose-repressed (7), gluconeogenic pck gene (11, 12, 19, 21, 27), encoding phosphoenolpyruvate carboxykinase (PCK) (derepressed via a point mutation in the promoter region), to replace the native phosphoenolpyruvate carboxylase (ppc) and serve as the primary route for CO₂ fixation (Fig. ​(Fig.1).1). A second acquired mutation was also identified as a frameshift mutation in the carboxy terminus of ptsI, inactivating the phosphoenolpyruvate-dependent phosphotransferase system (33). Glucose uptake by the phosphotransferase system was functionally replaced by galactose permease (galP) and glucokinase (glk).Open in a separate windowFIG. 1.Anaerobic metabolism of E. coli using the mixed-acid fermentation pathway (data from reference 1). The native phosphotransferase system pathway for glucose uptake and the mixed-acid pathway for fermentation are shown with black arrows. Peripheral reactions for glucose uptake, carboxylation, and acetyl-CoA synthesis are shown as dotted green arrows and represent new metabolic functions that have been recruited for succinate production from glucose. Reactions that have been blocked by gene deletions or point mutations are marked with an X. pck* indicates a novel mutation that derepressed pck, allowing the enzyme to serve as the primary route for oxaloacetate production. Pyruvate (boxed) appears at two sites but is presumed to exist as a single intracellular pool.Based on these previous studies, we have now determined the core mutations needed to direct carbon flow from glucose to succinate in E. coli and have constructed new succinate-producing strains with a minimum of genetic change.