Genetic Analysis of the nuo Locus,Which Encodes the Proton-Translocating NADH Dehydrogenase in Escherichia coli

Complex I (EC 1.6.99.3) of the bacterium Escherichia coli is considered to be the minimal form of the type I NADH dehydrogenase, the first enzyme complex in the respiratory chain. Because of its small size and relative simplicity, the E. coli enzyme has become a model used to identify and characterize the mechanism(s) by which cells regulate the synthesis and assembly of this large respiratory complex. To begin dissecting the processes by which E. coli cells regulate the expression of nuo and the assembly of complex I, we undertook a genetic analysis of the nuo locus, which encodes the 14 Nuo subunits comprising E. coli complex I. Here we present the results of studies, performed on an isogenic collection of nuo mutants, that focus on the physiological, biochemical, and molecular consequences caused by the lack of or defects in several Nuo subunits. In particular, we present evidence that NuoG, a peripheral subunit, is essential for complex I function and that it plays a role in the regulation of nuo expression and/or the assembly of complex I.

Complex I (NADH:ubiquinone oxidoreductase; EC 1.6.99.3), a type I NADH dehydrogenase that couples the oxidation of NADH to the generation of a proton motive force, is the first enzyme complex of the respiratory chain (2, 35, 47). The Escherichia coli enzyme, considered to be the minimal form of complex I, consists of 14 subunits instead of the 40 to 50 subunits associated with the homologous eukaryotic mitochondrial enzyme (17, 29, 30, 48–50). E. coli also possesses a second NADH dehydrogenase, NDH-II, which does not generate a proton motive force (31). E. coli complex I resembles eukaryotic complex I in many ways (16, 17, 30, 49): it performs the same enzymatic reaction and is sensitive to a number of the same inhibitors, it consists of subunits homologous to those found in all proton-translocating NADH:ubiquinone oxidoreductases studied thus far, it is comprised of a large number of subunits relative to the number that comprise other respiratory enzymes, and it contains flavin mononucleotide and FeS center prosthetic groups. Additionally, it possesses an L-shaped topology (14, 22) like that of its Neurospora crassa homolog (27), and it consists of distinct fragments or subcomplexes. Whereas eukaryotic complex I can be dissected into a peripheral arm and a membrane arm, the E. coli enzyme consists of three subcomplexes referred to as the peripheral, connecting, and membrane fragments (29) (Fig. ​(Fig.1A).1A). The subunit composition of these three fragments correlates approximately with the organization of the 14 structural genes (nuoA to nuoN) (49) of the nuo (for NADH:ubiquinone oxidoreductase) locus (Fig. ​(Fig.1B),1B), an organization that is conserved in several other bacteria, including Salmonella typhimurium (3), Paracoccus denitrificans (53), Rhodobacter capsulatus (12), and Thermus thermophilus (54). The 5′ half of the locus contains a promoter (nuoP), previously identified and located upstream of nuoA (8, 49), and the majority of genes that encode subunits homologous to the nucleus-encoded subunits of eukaryotic complex I and to subunits of the Alcaligenes eutrophus NAD-reducing hydrogenase (17, 29, 30, 49). In contrast, the 3′ half contains the majority of the genes that encode subunits homologous to the mitochondrion-encoded subunits of eukaryotic complex I and to subunits of the E. coli formate-hydrogen lyase complex (17, 29, 30, 49). Whereas the nuclear homologs NuoE, NuoF, and NuoG constitute the peripheral fragment (also referred to as the NADH dehydrogenase fragment [NDF]), the nuclear homologs NuoB, NuoC, NuoD, and NuoI constitute the connecting fragment. The mitochondrial homologs NuoA, NuoH, NuoJ, NuoK, NuoL, NuoM, and NuoN constitute the membrane fragment (29). E. coli complex I likely evolved by fusion of preexisting protein assemblies constituting modules for electron transfer and proton translocation (17–19, 30). Open in a separate windowFIG. 1Schematic of E. coli complex I and the nuo locus. Adapted with permission of the publisher (17, 29, 30, 49). (A) E. coli complex I is comprised of three distinct fragments: the peripheral (light gray), connecting (white), and membrane (dark gray) fragments (17, 29). The peripheral fragment (NDF) is comprised of the nuclear homologs NuoE, -F, and -G and exhibits NADH dehydrogenase activity that oxidizes NADH to NAD⁺; the connecting fragment is comprised of the nuclear homologs NuoB, -C, -D, and -I; and the membrane fragment is comprised of the mitochondrial homologs NuoA, -H, and -J to -N and catalyzes ubiquinone (Q) to its reduced form (QH₂). FMN, flavin mononucleotide. (B) The E. coli nuo locus encodes the 14 Nuo subunits that constitute complex I. The 5′ half of the locus contains a previously identified promoter (nuoP) and the majority of genes that encode the peripheral and connecting subunits (light gray and white, respectively). The 3′ half of the locus contains the majority of the genes encoding the membrane subunits (dark gray). The 3′ end of nuoG encodes a C-Terminal region (CTR) of the NuoG subunit (hatched).Because of its smaller size and relative simplicity, researchers recently have begun to utilize complex I of E. coli, and that of its close relative S. typhimurium, to identify and characterize the mechanism(s) by which cells regulate the synthesis and assembly of this large respiratory complex (3, 8, 46) and to investigate the diverse physiological consequences caused by defects in this enzyme (4, 6, 10, 40, 59). Such defects affect the ability of cells to perform chemotaxis (40), to grow on certain carbon sources (4, 6, 10, 40, 57), to survive stationary phase (59), to perform energy-dependent proteolysis (4), to regulate the expression of at least one gene (32), and to maintain virulence (5).To begin dissecting the processes by which E. coli cells regulate the expression of nuo and the assembly of complex I, we undertook a genetic analysis of the nuo locus. Here, we present the results of studies, performed on an isogenic collection of nuo mutants, that focus on the physiological, biochemical, and molecular consequences caused by the lack of or defects in several Nuo subunits. In particular, we present evidence that NuoG, a peripheral subunit, is essential for complex I function and that it plays a role in the regulation of nuo expression and/or the assembly of complex I.     

Endogenous 3,4-Dihydroxyphenylalanine and Dopaquinone Modifications on Protein Tyrosine: LINKS TO MITOCHONDRIALLY DERIVED OXIDATIVE STRESS VIA HYDROXYL RADICAL*

Oxidative modifications of protein tyrosines have been implicated in multiple human diseases. Among these modifications, elevations in levels of 3,4-dihydroxyphenylalanine (DOPA), a major product of hydroxyl radical addition to tyrosine, has been observed in a number of pathologies. Here we report the first proteome survey of endogenous site-specific modifications, i.e. DOPA and its further oxidation product dopaquinone in mouse brain and heart tissues. Results from LC-MS/MS analyses included 50 and 14 DOPA-modified tyrosine sites identified from brain and heart, respectively, whereas only a few nitrotyrosine-containing peptides, a more commonly studied marker of oxidative stress, were detectable, suggesting the much higher abundance for DOPA modification as compared with tyrosine nitration. Moreover, 20 and 12 dopaquinone-modified peptides were observed from brain and heart, respectively; nearly one-fourth of these peptides were also observed with DOPA modification on the same sites. For both tissues, these modifications are preferentially found in mitochondrial proteins with metal binding properties, consistent with metal-catalyzed hydroxyl radical formation from mitochondrial superoxide and hydrogen peroxide. These modifications also link to a number of mitochondrially associated and other signaling pathways. Furthermore, many of the modification sites were common sites of previously reported tyrosine phosphorylation, suggesting potential disruption of signaling pathways. Collectively, the results suggest that these modifications are linked with mitochondrially derived oxidative stress and may serve as sensitive markers for disease pathologies.Generation of reactive oxygen species (ROS)¹ and reactive nitrogen species is a normal consequence of aerobic metabolism that, in excess, results in oxidative stress that further leads to oxidative modification of proteins, lipids, and DNA, events that may lead to altered cellular function and even cell death (1, 2). Chronic oxidative stress is well recognized as having a central role in disease and is responsible for both direct alteration of biomolecular structure-function and compensatory changes in cellular processes (1–4). It is increasingly recognized that oxidative modifications of proteins can serve as potential biomarkers indicative of the physiological states and changes that occur during disease progression. Thus, the ability to quantitatively measure specific protein oxidation products has the potential to provide the means to monitor the physiological state of a tissue or organism, in particular any progression toward pathology. Given Parkinson disease (PD) as an example, a number of oxidative modifications on proteins pertinent to PD have been identified, further supporting the potential importance of oxidative modifications to disease pathogenesis (5).Many oxidative modifications on specific amino acid residues, such as protein carbonylation (6), cysteine S-nitrosylation (7–9), cysteine oxidation to sulfinic or sulfonic acid (10–12), methionine oxidation (13, 14), and tyrosine nitration (15–21) within complex protein mixtures, have been detected by MS-based proteomics; however, their low abundance levels within complex proteomes often hinder confident identification of these potentially significant modifications (22). For example, tyrosine nitration is a well studied post-translational modification mediated by peroxynitrite (ONOO⁻) or nitrogen dioxide (^·NO₂), which commonly occur in cells during oxidative stress and inflammation; however, only a small number of nitrotyrosine proteins have been identified from a given proteome sample because of insufficient analytical sensitivity and the chance of incorrect peptide assignments (19, 23). With recent advances in high resolution MS that provide high mass measurement accuracy, the ability to confidently identify modified peptides has been significantly enhanced (24).Hydroxyl radical (HO^·) is one of the most reactive and major species generated under aerobic conditions in biological systems (1, 25, 26). Among several HO^·-mediated oxidative modifications, the protein tyrosine modification 3,4-dihydroxyphenylalanine (DOPA) has been reported as a major product and index of HO^· attack on tyrosine residues in proteins (Fig. 1) (27, 28). DOPA is also formed on protein tyrosine residues via controlled enzymatic pathways through enzymes such as tyrosinase or tyrosine hydroxylase (28). Once formed, protein-bound DOPA has the potential to initiate further oxidative reactions through binding and reducing transition metals or through redox cycling between catechol and quinone (dopaquinone) forms (29, 30). Recent studies have suggested that protein-bound DOPA is involved in triggering antioxidant defenses (30) and mediating oxidative damage to DNA (31). Moreover, elevated levels of protein-bound DOPA have been reported in several diseases, including atherosclerosis, cataracts, and myocardial disease, and in PD patients undergoing levodopa therapy (26, 32–36). However, the specific DOPA-modified proteins, which could provide mechanistic knowledge of the progression of these diseases, have not been identified (27, 28). The ability to identify site-specific protein modifications should lead to a better understanding of the role of DOPA modification in disease pathologies as well as new molecular signatures or therapeutic targets for diseases.Open in a separate windowFig. 1.DOPA and dopaquinone formation from tyrosine.Therefore, in this study, we demonstrate the ability to identify site-specific DOPA and dopaquinone (DQ) modifications on protein tyrosine residues in normal mouse brain and heart tissues and their relative stoichiometries that are present in vivo under non-stressed conditions. Such endogenous protein modifications were detected using LC-MS/MS. The results from this global proteomics survey suggests that HO^· in tissues under normal conditions is generated largely from the mitochondria and metal-binding proteins where the resulting DOPA/DQ modifications have the potential to disrupt mitochondrial respiration as well as alter tyrosine phosphorylation signaling pathways such as 14-3-3-mediated signaling in brain tissue.     

Increased Protein Stability of FGF1 Can Compensate for Its Reduced Affinity for Heparin

Human FGF1 (fibroblast growth factor 1) is a powerful signaling molecule with a short half-life in vivo and a denaturation temperature close to physiological. Binding to heparin increases the stability of FGF1 and is believed to be important in the formation of FGF1·fibroblast growth factor receptor (FGFR) active complex. In order to reveal the function of heparin in FGF1·FGFR complex formation and signaling, we constructed several FGF1 variants with reduced affinity for heparin and with diverse stability. We determined their biophysical properties and biological activities as well as their ability to translocate across cellular membranes. Our study showed that increased thermodynamic stability of FGF1 nicely compensates for decreased binding of heparin in FGFR activation, induction of DNA synthesis, and cell proliferation. By stepwise introduction of stabilizing mutations into the K118E (K132E) FGF1 variant that shows reduced affinity for heparin and is inactive in stimulation of DNA synthesis, we were able to restore the full mitogenic activity of this mutant. Our results indicate that the main role of heparin in FGF-induced signaling is to protect this naturally unstable protein against heat and/or proteolytic degradation and that heparin is not essential for a direct FGF1-FGFR interaction and receptor activation.FGF1 (fibroblast growth factor 1) belongs to a family of polypeptide growth factors comprising in humans 22 structurally related proteins (1, 2). The signaling induced by the growth factor leads to a wide range of cellular responses during development as well as in adult life, such as growth regulation, differentiation, survival, stress response, migration, and proliferation of different cell types (3). The biological activity of FGF1 is exerted through binding to four high affinity cell surface receptors (FGFR1–4), resulting in receptor dimerization and transphosphorylation in its tyrosine kinase domain (4, 5). The activated FGFR³ induces cellular response by initiating several signaling cascades, including mitogen-activated protein kinase (MAPK), phosphoinositide 3-kinase/Akt, and phospholipase C-γ (PLC-γ) pathways (6).In addition to FGFRs, FGF1 binds to heparan sulfates (HS) associated with proteoglycans at the cell surface and in the extracellular matrix (7). Among the physiological sugars, the highest affinity for FGF1 is shown by heparin, a widely used linear, highly sulfated polysaccharide composed of 2-O-sulfated iduronic acid and 6-O-sulfated, N-sulfated glucosamine units (8).Despite many years of research, there is still controversy regarding the molecular role of heparin/HS in FGF1- and FGF2-induced signaling. Thus, the question of whether or not the linkage of two molecules of the growth factor by heparin/HS is an absolute prerequisite for induction of FGFR dimerization is still open. Numerous studies have concluded that the presence of heparin/HS is obligatory for FGF signaling. It is widely believed that heparin/HS is directly involved in receptor dimerization and is critical for mitogenic response stimulated by the growth factor (4, 6, 8–10).On the other hand, several authors working on FGF1 and FGF2 have suggested that there is no mandatory requirement for heparin for the assembly and activation of the FGF·FGFR complex. They imply that heparin only plays a role in association of two molecules of the growth factor and therefore facilitates their binding to FGFR (11). It has been reported that FGF1 and FGF2 can interact with the FGFR and trigger phosphorylation of p42/44 MAPK and activation of other signaling pathways even in the absence of HS (12–16).The accepted role of heparin/HS in FGF1 signaling is to prevent the degradation of the growth factor (17). The interaction with heparin or HS protects FGF1 against heat, acidic pH, and proteases (18, 19). HS also seems to regulate the activity of different FGFs by creating their local reservoir and generating a concentration gradient of the growth factor (6, 17).The binding of FGF1 to heparin/HS is mediated by specific residues forming a positively charged patch on the protein surface (20, 21). The major contribution is made by Lys¹¹⁸ (Lys¹³² in the full-length numbering system), which was identified by Harper and Lobb (22), and Lys¹¹² and Arg¹²² (23, 24). Additional residues of FGF1 involved in the interaction with heparin are the positively charged Lys¹¹³, Arg¹¹⁹, and Lys¹²⁸ and the polar Asn¹⁸, Asn¹¹⁴, and Gln¹²⁷ (20, 21). Site-directed mutagenesis and other studies have revealed the importance of Lys¹¹⁸ not only in heparin binding but also for the biological function of FGF1 (22, 25, 26). It was shown that the K118E (K132E) mutant is inactive in stimulation of DNA synthesis, although its affinity for FGFR and the ability to activate signaling cascades is not reduced (27, 28). Despite extensive research, the reason for the lack of mitogenic potential of K118E FGF1 is still not clear.In this paper, we verified the function of heparin in FGF1·FGFR complex formation and signaling by constructing several FGF1 mutants with reduced affinity for heparin. To recover the stability of these variants, which could no longer be stabilized by heparin, we supplemented them stepwise with stabilizing mutations (29). We analyzed thoroughly their biological activity and their ability to translocate across cellular membranes (30–34). Interestingly, the full mitogenic activity of the K118E FGF1 variant was restored by the introduced stabilizing mutations.Our results indicate that the main role of heparin in FGF-induced signaling is to protect this naturally unstable protein against heat denaturation and proteolytic degradation and that the increased stability of the growth factor can compensate for reduced heparin binding.     

Direct Fe2+ Sensing by Iron-responsive Messenger RNA��Repressor Complexes Weakens Binding

Fe²⁺ is now shown to weaken binding between ferritin and mitochondrial aconitase messenger RNA noncoding regulatory structures ((iron-responsive element) (IRE)-RNAs) and the regulatory proteins (IRPs), which adds a direct role of iron to regulation that can complement the well known regulatory protein modification and degradative pathways related to iron-induced mRNA translation. We observe that the K_d value increases 17-fold in 5′-untranslated region IRE-RNA·repressor complexes; Fe²⁺, is studied in the absence of O₂. Other metal ions, Mn²⁺ and Mg²⁺ have similar effects to Fe²⁺ but the required Mg²⁺ concentration is 100 times greater than for Fe²⁺ or Mn²⁺. Metal ions also weaken ethidium bromide binding to IRE-RNA with no effect on IRP fluorescence, using Mn²⁺ as an O₂-resistant surrogate for Fe²⁺, indicating that metal ions bound IRE-RNA but not IRP. Fe²⁺ decreases IRP repressor complex stability of ferritin IRE-RNA 5–10 times compared with 2–5 times for mitochondrial aconitase IRE-RNA, over the same concentration range, suggesting that differences among IRE-RNA structures contribute to the differences in the iron responses observed in vivo. The results show the IRE-RNA·repressor complex literally responds to Fe²⁺, selectively for each IRE-mRNA.Iron (e.g. ferrous sulfate, ferric citrate, and hemin) added to animal cells changes translation rates of messenger RNAs encoding proteins of iron traffic and oxidative metabolism (1–4). To cross cell membranes, iron ions are transported by membrane proteins such as DMT1 or carried on proteins such as transferrin. Inside the cells, iron is mainly in heme, FeS clusters, non-heme iron cofactors of proteins, and iron oxide minerals coated by protein nanocages (ferritins). Iron in transit is thought to be Fe²⁺ in labile “pools” accessible to small molecular weight chelators, and/or bound loosely by chaperones.When iron concentrations in the cells increase, a group of mRNAs with three-dimensional, noncoding structures in the 5′-untranslated region (UTR)³ are derepressed (Fig. 1A), i.e. the fraction of the mRNAs in mRNA·repressor protein complexes, which inhibit ribosome binding, decreases and the fraction of the mRNAs in polyribosomes increases (5–7). The three-dimensional, noncoding mRNA structure, representing a family of related structures, is called the iron-responsive element, or IRE, and the repressors are called iron regulatory proteins (IRPs). Together they are one of the most extensively studied eukaryotic messenger RNA regulatory systems (1–4). In addition to large numbers of cell studies, structures of IRE-RNAs are known from solution NMR (8–12), and the RNA·protein complex from x-ray crystallography (13). Recent data indicate that demetallation of IRP1 and disruption of the [4Fe-4S] cluster that inhibits IRP1 binding to RNA will be enhanced by phosphorylation and low iron concentrations (1, 2, 14–16). Such results can explain the increased IRP1 binding to IRE-mRNAs and increased translational repression when iron concentrations are abnormally low. However, the mechanism to explain dissociation of IRE-RNA·IRP complexes, thereby allowing ribosome assembly and increased proteosomal degradation of IRPs (1, 2, 14, 15) (Fig. 1A), when high iron concentrations are abnormally high, is currently unknown.Open in a separate windowFIGURE 1.IRE-RNA·IRP complexes and a model for depression by excess iron. A, a representative model of iron-induced translation of 5′-UTR IRE-RNAs. This figure is modified from Ref. 7. B, IRE-RNA sites influenced by metal binding related to the crystal structure of the ferritin-IRE-RNA·IRP complex from Ref. 13. The figure was created by T. Tosha using Discovery Studio 1.6 and Protein Data Bank file 2IPY. ■, hydrated Mg²⁺, determined by solution NMR; ▴, Cu¹⁺-1.10-phenanthroline, determined by RNA cleavage in O₂.Metal ion binding changes conformation and function of most RNA classes, e.g. rRNA (17), tRNA (18, 19), ribozymes (20–23), riboswitches (24, 25), possibly hammerhead mRNAs in mammals (26), and proteins. Although the effects of metal ion binding on eukaryotic mRNAs have not been extensively studied, Mg²⁺ is known to cause changes in conformation, shown by changes in radical cleavage sites of IRE-RNA with 1,10-phenanthrolene-iron and proton shifts in the one-dimensional NMR spectrum (12, 27). The Mg²⁺ effects are observed at low magnesium concentrations (0.1–0.5 mm) and low molar stoichiometries (1:1 and 2:1 = Mg:RNA).We hypothesized that Fe²⁺ could directly change the binding of the IRE-mRNA to the iron regulatory protein for several reasons. First, other metal ions influence the IRE-RNA structure (12, 27). Second, in IRE-RNA/IRP cocrystals there are exposed RNA sites in the IRE-RNA/IRP complex that are accessible for interactions (13) (Fig. 1B). Third, regions in the IRE-RNA are hypersensitive to Fe²⁺-EDTA/ascorbate/H₂O₂, suggesting selective interactions with metals and/or solvent (28). We now report that Fe²⁺ weakens IRE-RNA/IRP binding, whereas Mg²⁺ requires 100 times the concentration and Mn²⁺ is comparable with Fe²⁺; the Fe²⁺ effect was diminished in mutant IRE-RNA and IRE-RNA selective in wild type sequences: ferritin IRE-RNA > mt-aconitase IRE-RNA.     

Printor, a Novel TorsinA-interacting Protein Implicated in Dystonia Pathogenesis

Early onset generalized dystonia (DYT1) is an autosomal dominant neurological disorder caused by deletion of a single glutamate residue (torsinA ΔE) in the C-terminal region of the AAA⁺ (ATPases associated with a variety of cellular activities) protein torsinA. The pathogenic mechanism by which torsinA ΔE mutation leads to dystonia remains unknown. Here we report the identification and characterization of a 628-amino acid novel protein, printor, that interacts with torsinA. Printor co-distributes with torsinA in multiple brain regions and co-localizes with torsinA in the endoplasmic reticulum. Interestingly, printor selectively binds to the ATP-free form but not to the ATP-bound form of torsinA, supporting a role for printor as a cofactor rather than a substrate of torsinA. The interaction of printor with torsinA is completely abolished by the dystonia-associated torsinA ΔE mutation. Our findings suggest that printor is a new component of the DYT1 pathogenic pathway and provide a potential molecular target for therapeutic intervention in dystonia.Early onset generalized torsion dystonia (DYT1) is the most common and severe form of hereditary dystonia, a movement disorder characterized by involuntary movements and sustained muscle spasms (1). This autosomal dominant disease has childhood onset and its dystonic symptoms are thought to result from neuronal dysfunction rather than neurodegeneration (2, 3). Most DYT1 cases are caused by deletion of a single glutamate residue at positions 302 or 303 (torsinA ΔE) of the 332-amino acid protein torsinA (4). In addition, a different torsinA mutation that deletes amino acids Phe³²³–Tyr³²⁸ (torsinA Δ323–328) was identified in a single family with dystonia (5), although the pathogenic significance of this torsinA mutation is unclear because these patients contain a concomitant mutation in another dystonia-related protein, ϵ-sarcoglycan (6). Recently, genetic association studies have implicated polymorphisms in the torsinA gene as a genetic risk factor in the development of adult-onset idiopathic dystonia (7, 8).TorsinA contains an N-terminal endoplasmic reticulum (ER)³ signal sequence and a 20-amino acid hydrophobic region followed by a conserved AAA⁺ (ATPases associated with a variety of cellular activities) domain (9, 10). Because members of the AAA⁺ family are known to facilitate conformational changes in target proteins (11, 12), it has been proposed that torsinA may function as a molecular chaperone (13, 14). TorsinA is widely expressed in brain and multiple other tissues (15) and is primarily associated with the ER and nuclear envelope (NE) compartments in cells (16–20). TorsinA is believed to mainly reside in the lumen of the ER and NE (17–19) and has been shown to bind lamina-associated polypeptide 1 (LAP1) (21), lumenal domain-like LAP1 (LULL1) (21), and nesprins (22). In addition, recent evidence indicates that a significant pool of torsinA exhibits a topology in which the AAA⁺ domain faces the cytoplasm (20). In support of this topology, torsinA is found in the cytoplasm, neuronal processes, and synaptic terminals (2, 3, 15, 23–26) and has been shown to bind cytosolic proteins snapin (27) and kinesin light chain 1 (20). TorsinA has been proposed to play a role in several cellular processes, including dopaminergic neurotransmission (28–31), NE organization and dynamics (17, 22, 32), and protein trafficking (27, 33). However, the precise biological function of torsinA and its regulation remain unknown.To gain insights into torsinA function, we performed yeast two-hybrid screens to search for torsinA-interacting proteins in the brain. We report here the isolation and characterization of a novel protein named printor (protein interactor of torsinA) that interacts selectively with wild-type (WT) torsinA but not the dystonia-associated torsinA ΔE mutant. Our data suggest that printor may serve as a cofactor of torsinA and provide a new molecular target for understanding and treating dystonia.     

Motogenic Sites in Human Fibronectin Are Masked by Long Range Interactions

Fibronectin (FN) is a large extracellular matrix glycoprotein important for development and wound healing in vertebrates. Recent work has focused on the ability of FN fragments and embryonic or tumorigenic splicing variants to stimulate fibroblast migration into collagen gels. This activity has been localized to specific sites and is not exhibited by full-length FN. Here we show that an N-terminal FN fragment, spanning the migration stimulation sites and including the first three type III FN domains, also lacks this activity. A screen for interdomain interactions by solution-state NMR spectroscopy revealed specific contacts between the Fn N terminus and two of the type III domains. A single amino acid substitution, R222A, disrupts the strongest interaction, between domains ^4–5FnI and ³FnIII, and restores motogenic activity to the FN N-terminal fragment. Anastellin, which promotes fibril formation, destabilizes ³FnIII and disrupts the observed ^4–5FnI-³FnIII interaction. We discuss these findings in the context of the control of cellular activity through exposure of masked sites.Fibronectin (FN),4 a large multidomain glycoprotein found in all vertebrates, plays a vital role in cell adhesion, tissue development, and wound healing (1). It exists in soluble form in plasma and tissue fluids but is also present in fibrillar networks as part of the extracellular matrix. The structures of many FN domains of all three types, FnI, FnII, and FnIII, are known, for example (2–4). Although interactions between domains that are close in primary sequence have been demonstrated (3, 5), studies of multidomain fragments generally assume a beads-on-string model (2). There is, however, much evidence for the presence of long range order in soluble FN as a number of functional sites, termed cryptic, are not active in the native molecule, until exposed through conformational change. These include self-association sites (5–8), sites of protein interactions (9), and sites that control cellular activity (10, 11). Low resolution studies of the FN dimer suggest a compact conformation under physiological conditions (12–14); however, attempts to define large scale structure in FN by small angle scattering or electric birefringence (15–17) have yielded contradictory results. Interpretation of domain stability changes in terms of interaction sites (18) has also not been straightforward (2), possibly because of domain stabilization through nearest-neighbor effects (19, 20).A FN splicing variant produced in fetal and cancer patient fibroblasts, termed migration stimulation factor (MSF), stimulates migration of adult skin fibroblasts into type I collagen gels (10, 21) and breast carcinoma cells using the Boyden chamber (22). MSF comprises FN domains ¹FnI to ⁹FnI, a truncated ¹FnIII, and a small C-terminal extension; a recombinant FN fragment corresponding to ¹FnI-⁹FnI (Fn70kDa) displays the same activity (10). An overview of FN domain structure and nomenclature is presented in Fig. 1a. Further experiments sub-localized full motogenic activity to the gelatin binding domain of FN (GBD, domains ⁶FnI-⁹FnI) (23) and partial activity to a shorter fragment spanning domains ^7–9FnI (24). Two IGD tripeptides of domains ⁷FnI and ⁹FnI were shown to be essential through residue substitutions and reconstitution of partial motogenic activity in synthetic peptides (10, 24, 25); however, similar IGD tripeptides outside the GBD, on domains ³FnI and ⁵FnI, appear to have little effect (10, 23). Full-length adult FN does not affect cell migration in similar assays (10, 23); thus motogenic activity sites are presumed to be masked in the conformation adopted by soluble FN, although they could be exposed by molecular rearrangement.Open in a separate windowFIGURE 1.Motogenic activity of FN fragments. a, schematic representation of the FN domain structure (top) and enlargement of the FN N terminus (bottom). Type I domains are shown as pentagons; type II domains as hexagons; and type III domains as ovals. b, comparison of motogenic activity versus protein concentration of wild-type Fn70kDa and Fn100kDa fragments. Error bars are derived from duplicate experiments, and a gray band denotes migration activity of media without additives. c, similar comparisons for mutant Fn100kDa fragments. d, analytical size exclusion chromatography of large FN fragments. The trace of UV absorbance at 280 nm versus elution volume shown here indicates a larger hydrodynamic radius for Fn100kDa R222A compared with the wild type, consistent with our model (Fig. 6a).Here we show that a recombinant fragment, closely matching a truncated form of FN identified in zebrafish (26), as well as amphibians, birds, and mammals (27), does not stimulate cell migration. This fragment is similar to MSF but includes the first three FnIII domains (^1–3FnIII), suggesting that these domains are responsible for a conformational transition that masks the activity sites in this construct and probably in full-length FN. To identify the mechanism behind this transition, we performed structural studies by solution NMR spectroscopy and identified a specific long range interaction between domains ^4–5FnI and ³FnIII as essential for this masking effect. Interestingly, this interaction does not involve direct contacts with the GBD but possibly represses motogenic activity through chain compaction, evident in analytical size exclusion assays. Intramolecular interactions thus provide a mechanism by which conformational rearrangement induced, for example, by tension or splicing variation can result in cellular activity differences.     

Enzymatic Conversion of Glucose to UDP-4-Keto-6-Deoxyglucose in Streptomyces spp.

All of the 2,6-dideoxy sugars contained within the structure of chromomycin A₃ are derived from d-glucose. Enzyme assays were used to confirm the presence of hexokinase, phosphoglucomutase, UDPG pyrophosphorylase (UDPGP), and UDPG oxidoreductase (UDPGO), all of which are involved in the pathway of glucose activation and conversion into 2,6-dideoxyhexoses during chromomycin biosynthesis. Levels of the four enzymes in Streptomyces spp. cell extracts were correlated with the production of chromomycins. The pathway of sugar activation in Streptomyces spp. involves glucose 6-phosphorylation by hexokinase, isomerization to G-1-P catalyzed by phosphoglucomutase, synthesis of UDPG catalyzed by UDPGP, and formation of UDP-4-keto-6-deoxyglucose by UDPGO.Dideoxy sugars occur commonly in the structures of cardiac glycosides from plants, in antibiotics like chromomycin A₃ (Fig. ​(Fig.1),1), and in macrolides produced by microorganisms. On the basis of stable isotope-labeling experiments, biosynthetic studies conducted in Rosazza’s laboratory have indicated that all the deoxy sugars of chromomycin A₃ are derived from d-glucose (21). While the assembly of the polyketide aglycone is reasonably well understood, relatively little is known of the details of 2,6-dideoxy sugar biogenesis in streptomycetes. Earlier studies with Streptomyces rimosus indicated that TDP-mycarose is synthesized from TDP-d-glucose (TDPG) and S-adenosyl-l-methionine (10, 23). The reaction requires NADPH as a cofactor, and TDP-4-keto-6-deoxy-d-glucose is an intermediate. Formation of TDP-4-keto-6-deoxy-d-glucose was catalyzed by the enzyme TDPG oxidoreductase (TDPG-4,6-dehydratase; EC 4.2.1.46). Similar 4-keto sugar nucleotides are intermediates for the biosynthesis of polyene macrolide antibiotic amino sugars (18). Similar pathways have been elaborated for the formation of 2,6-dideoxy-d-threo-4-hexulose of granaticin in Escherichia coli (6, 25) and 2,6-dideoxy-d-arabino-hexose of chlorothricin (12). The initial 6-deoxygenation of glucose during 3,6-dideoxy sugar formation involves a similar mechanism (32). In all of these processes, glucose is first activated by conversion into a sugar nucleotide such as UDPG followed by NAD⁺ oxidation of the 4 position to the corresponding 4-oxo derivative. Position 6 deoxygenation involves a general tautomerization, dehydration, and NADH,H⁺-catalyzed reduction process (6, 12, 25). A similar tautomerization and dehydration followed by reduction may produce C-3-deoxygenated products, such as CDP-3,6-dideoxyglucose (27). The pathway for formation of 3,6-dideoxyhexoses from CDPG in Yersinia pseudotuberculosis was clearly elucidated by Liu and Thorson (14). However, none of this elegant work was focused on the earlier steps of hexose nucleotide formation. Open in a separate windowFIG. 1Structures of chromomycins A₂ and A₃.On the basis of previous work (7), it is reasonable to postulate that the biosynthesis of 2,6-dideoxyglucose in Streptomyces griseus involves phosphorylation to glucose-6-phosphate by hexokinase (HK; E.C.2.7.7.1), as in glycolysis; conversion to glucose-1-phosphate by phosphoglucomutase (PGM; EC 2.7.5.1); reaction with UTP to form UDPG in a reaction catalyzed by UDPG pyrophosphorylase (UDPGP) (glucose-1-phosphate uridylyltransferase; EC 2.7.7.9), and C-6 deoxygenation catalyzed by UDP-d-glucose-4,6-dehydratase with NAD⁺ as a cofactor (Fig. ​(Fig.2).2). UDPG and GDPG have been detected in cell extracts of S. griseus and Streptomyces sp. strain MRS202, suggesting that these compounds are active sugar nucleotides involved in the formation of dideoxyhexoses (15). UDPGP genes from several bacteria have been cloned and sequenced (1, 3, 4, 11, 29, 30). Although nucleotidyl diphosphohexose-4,6-dehydratases (NDP-hexose-4,6-dehydratases) have been purified and characterized from several sources (5, 8, 9, 13, 19, 25, 26, 31, 33), the occurrence of the glucose-activating enzymes HK, PGM, UDPGP, and UDPG oxidoreductase (UDPGO) involved in 2,6-dideoxyhexose formation has not been established in streptomycetes. This work provides evidence for the presence of these enzymes involved in the biosynthetic activation of glucose to the 2,6-dideoxyhexoses in chromomycin A₃.Open in a separate windowFIG. 2Proposed pathway for the formation of 2,6-dideoxy sugars in streptomycetes involving HK, PGM, UDPGP, and UDPGO.     

Studies on the DIDS-binding Site of Monocarboxylate Transporter 1 Suggest a Homology Model of the Open Conformation and a Plausible Translocation Cycle

Site-directed mutagenesis of MCT1 was performed on exofacial lysines Lys³⁸, Lys⁴⁵, Lys²⁸², and Lys⁴¹³. K38Q-MCT1 and K38R-MCT1 were inactive when expressed at the plasma membrane of Xenopus laevis oocytes, whereas K45R/K282R/K413R-MCT1 and K45Q/K282Q/K413Q-MCT1 were active. The former exhibited normal reversible and irreversible inhibition by DIDS, whereas the latter showed less reversible and no irreversible inhibition. K45Q/K413Q-MCT1 retained some irreversible inhibition, whereas K45Q/K282Q-MCT1 and K282Q/K413Q-MCT1 did not. These data suggest that the two DIDS SO₃⁻ groups interact with positively charged Lys²⁸² together with Lys⁴⁵ and/or Lys⁴¹³. This positions one DIDS isothiocyanate group close to Lys³⁸, leading to its covalent modification and irreversible inhibition. Additional mutagenesis revealed that DIDS cross-links MCT1 to its ancillary protein embigin using either Lys³⁸ or Lys²⁹⁰ of MCT1 and Lys¹⁶⁰ or Lys¹⁶⁴ of embigin. We have modeled a possible structure for the outward facing (open) conformation of MCT1 by employing modest rotations of the C-terminal domain of the inner facing conformation modeled previously. The resulting model structure has a DIDS-binding site consistent with experimental data and locates Lys³⁸ in a hydrophobic environment at the bottom of a substrate-binding channel. Our model suggests a translocation cycle in which Lys³⁸ accepts a proton before binding lactate. Both the lactate and proton are then passed through the channel via Asp³⁰²⁻ and Asp³⁰⁶⁺, an ion pair already identified as important for transport and located adjacent to Phe³⁶⁰, which controls channel selectivity. The cross-linking data have also been used to model a structure of MCT1 bound to embigin that is consistent with published data.Monocarboxylate transporter 1 (MCT1)³ is a member of the monocarboxylate transporter family (SLC16) of which there are 14 known members encoded by both the human and mouse genomes (1). All of the members of this family are thought to have 12 transmembrane alpha helices (TMs) with a large loop between TMs 6 and 7 and the C and N termini facing the cytosol (2, 3). The only members of the MCT family that have been shown to catalyze transport of monocarboxylates such as l-lactate across the plasma membrane are isoforms 1–4 (4–8). This transport is proton-linked and leads to the net uptake or release of lactic acid from cells, which is critical for metabolic pathways such as anaerobic glycolysis, gluconeogenesis, and lactate oxidation (9). MCT8 is a high affinity thyroid hormone transporter (10), whereas MCT10 (TAT1) is an aromatic amino acid transporter (11). The other members of the MCT family remain to be characterized.MCT1 is the most widely distributed member of the MCT family and was first identified as the lactate transporter present in red blood cells where its kinetics and substrate and inhibitor specificity were investigated in detail (9, 11, 12). These studies revealed that MCT1 can be inhibited by stilbene disulfonate derivatives such as DIDS and 4,4′-dibenzamido-stilbene-2,2′-disulfonate (DBDS). DIDS was shown to exhibit a rapid reversible inhibition of transport that was competitive with respect to l-lactate. This is followed by a slowly developing irreversible inhibition that is not exhibited by DBDS and is thought to be caused by one of the isothiocyanate groups of DIDS attacking a lysine residue on MCT1 (13–15). Prolonged incubation with DIDS also led to a fraction of the MCT1 becoming cross-linked to a 70-kDa glycoprotein that was identified as embigin, also known as gp70 (16). Embigin has a short intracellular C terminus, a single TM sequence containing a glutamic acid residue, and a large extracellular N terminus containing two immunoglobulin domains (17, 18). Subsequent studies revealed that either embigin or, more frequently, the homologous protein basigin (also known as CD147) is required as a chaperone to take MCT1 to the membrane (19) where the two proteins must remain associated for transport activity to be maintained (20, 21).Expression of MCTs 1, 2, and 4 in Xenopus laevis oocytes has enabled their further characterization and the effects of site-directed mutagenesis to be investigated (4, 5, 7, 8, 22–24). Such studies, together with homology modeling have enabled us to propose a three-dimensional structure of MCT1 based around the published structure of the Escherichia coli glycerol-3-phosphate transporter (Protein Data Bank 1PW4) (24). This model can account for the effects of mutating a range of amino acids, including some that disrupt the interaction with basigin, and has led to the proposal that the single TM of basigin or embigin lies between TMs 3 and 6 of MCT1. The model also reveals exofacial lysines that are present in MCT1 that might be responsible for the irreversible inhibition of MCT1 by DIDS and the cross-linking of MCT1 to embigin. In rat MCT1 these residues are Lys³⁸, Lys⁴⁵, Lys²⁸², Lys²⁸⁴, Lys²⁹⁰, and Lys⁴¹³. In this paper, we use site-directed mutagenesis of these lysine residues to identify which of them are involved in DIDS binding to MCT1. In addition we use site-directed mutagenesis of embigin to demonstrate that Lys¹⁶⁰ and Lys¹⁶⁴ are involved in its cross-linking to MCT1. Our new data allow us to propose a modified structural model of MCT1 in its outward facing conformation that binds DIDS. This model is consistent with the site-directed mutagenesis data and also suggests a mechanism for the translocation cycle that involves Lys³⁸ as well as Asp³⁰² and Arg³⁰⁶ that have already been identified as important for transport (23, 24). We have also been able to model a structure of MCT1 bound to embigin that is consistent with published data.     

Cloning and Expression of the Inositol Monophosphatase Gene from Methanococcus jannaschii and Characterization of the Enzyme

Inositol monophosphatase (EC 3.1.3.25) plays a pivotal role in the biosynthesis of di-myo-inositol-1,1′-phosphate, an osmolyte found in hyperthermophilic archaea. Given the sequence homology between the MJ109 gene product of Methanococcus jannaschii and human inositol monophosphatase, the MJ109 gene was cloned and expressed in Escherichia coli and examined for inositol monophosphatase activity. The purified MJ109 gene product showed inositol monophosphatase activity with kinetic parameters (K_m = 0.091 ± 0.016 mM; V_max = 9.3 ± 0.45 μmol of P_i min⁻¹ mg of protein⁻¹) comparable to those of mammalian and E. coli enzymes. Its substrate specificity, Mg²⁺ requirement, Li⁺ inhibition, subunit association (dimerization), and heat stability were studied and compared to those of other inositol monophosphatases. The lack of inhibition by low concentrations of Li⁺ and high concentrations of Mg²⁺ and the high rates of hydrolysis of glucose-1-phosphate and p-nitrophenylphosphate are the most pronounced differences between the archaeal inositol monophosphatase and those from other sources. The possible causes of these kinetic differences are discussed, based on the active site sequence alignment between M. jannaschii and human inositol monophosphatase and the crystal structure of the mammalian enzyme.The sole pathway for myo-inositol biosynthesis is the cyclization of glucose-6-phosphate to inositol-1-phosphate (I-1-P) by I-1-P synthase (EC 5.5.1.4) and the dephosphorylation of I-1-P by inositol monophosphatase (I-1-Pase; EC 3.1.3.25) (7–9, 12, 16, 24). This de novo pathway provides the ultimate source of free inositol for the cell. It is also a key enzyme involved in second-message signal transduction processes in mammalian and plant cells (2, 24, 28, 37). In phosphoinositide signaling (2, 37), I-1-Pase recycles the water-soluble phospholipase C phospholipid degradation products, inositol phosphates, to myo-inositol and helps to maintain a moderate inositol pool. Its inhibition by millimolar concentrations of lithium (19) has made it a putative target of lithium therapy for manic depression (34).Di-myo-inositol-1,1′-phosphate (DIP), a novel inositol phosphate compound found in hyperthermophilic archaea, including Pyrococcus woesei (43), Pyrococcus furiosus (41), Methanococcus igneus (11), and Thermotoga maritima (36), is used for osmotic balance at high growth temperatures. In order to understand what regulates its accumulation in cells, the DIP biosynthetic pathway must be well characterized in vitro. Based on ¹³C-labeling studies and assays of crude protein extracts from M. igneus (10), a pathway was proposed that converts glucose-6-phosphate to I-1-P (step 1), hydrolyzes some of the I-1-P to myo-inositol (step 2), and activates I-1-P to CDP-inositol (CDP-I) (step 3) for a final reaction (step 4) whereby CDP-I is coupled to myo-inositol, generating DIP and CMP (Fig. ​(Fig.1).1). Activities for I-1-P synthase, I-1-Pase, and DIP synthase in the DIP biosynthetic pathway have been detected in crude protein extracts of M. igneus (10). Phosphatase activities are ubiquitous in cells, and the observed activity in M. igneus could be due to a specific I-1-Pase activity or a nonspecific phosphatase. For mammalian and plant cells, I-1-Pases are all lithium sensitive and are inhibited at millimolar concentrations of Li⁺ (14, 15, 19, 30, 42). The partially purified phosphatase in M. igneus exhibited substrate specificity for dl-I-1-P over other sugar phosphates (10). It had an absolute requirement for Mg²⁺, a characteristic of all specific I-1-Pases studied thus far, and was also partially inhibited by Li⁺, though at a much higher concentration (160 mM for 50% activity inhibition) than reported for I-1-Pases from other cells. While this was suggestive of a specific I-1-Pase, the same protein fractions demonstrated considerable activity toward p-nitrophenylphosphate (pNPP), a very poor substrate for mammalian enzymes (1, 14). These preliminary characterizations of phosphatase activity suggested that archaeal I-1-Pases might be different from mammalian and plant enzymes. Open in a separate windowFIG. 1Proposed DIP biosynthetic pathway. Glucose-6-phosphate is converted to I-1-P (step 1), some of which is hydrolyzed to myo-inositol (step 2), and I-1-P is activated to CDP-I (step 3) for a final reaction in which CDP-I is coupled to myo-inositol (step 4), generating DIP and CMP.Methanococcus jannaschii was the first archaeon whose complete genomic sequence was determined (6). Of all the archaea with sequenced genomes, it is the closest to M. igneus. MJ109 encodes a 252-amino-acid protein that is highly homologous to both I-1-Pase and extragenic suppressor (the suhB gene product) (6). The latter gene product cloned in E. coli also has I-1-Pase activity (29). The putative identification of the MJ109 gene product as an I-1-Pase prompted us to express the gene product in E. coli and to examine its specific activity toward a variety of phosphate esters. The protein produced in this fashion clearly has I-1-Pase activity and shows several striking differences from plant and mammalian I-1-Pase activities.     

Resistance of Human Cytomegalovirus to Benzimidazole Ribonucleosides Maps to Two Open Reading Frames: UL89 and UL56

2,5,6-Trichloro-1-β-d-ribofuranosyl benzimidazole (TCRB) is a potent and selective inhibitor of human cytomegalovirus (HCMV) replication. TCRB acts via a novel mechanism involving inhibition of viral DNA processing and packaging. Resistance to the 2-bromo analog (BDCRB) has been mapped to the UL89 open reading frame (ORF), and this gene product was proposed as the viral target of the benzimidazole nucleosides. In this study, we report the independent isolation of virus that is 20- to 30-fold resistant to TCRB (isolate C4) and the characterization of the virus. The six ORFs known to be essential for viral DNA cleavage and packaging (UL51, UL52, UL56, UL77, UL89, and UL104) were sequenced from wild-type HCMV, strain Towne, and from isolate C4. Mutations were identified in UL89 (D344E) and in UL56 (Q204R). The mutation in UL89 was identical to that previously reported for virus resistant to BDCRB, but the mutation in UL56 is novel. Marker transfer analysis demonstrated that each of these mutations individually caused ∼10-fold resistance to the benzimidazoles and that the combination of both mutations caused ∼30-fold resistance. The rate and extent of replication of the mutants was the same as for wild-type virus, but the viruses were less sensitive to inhibition of DNA cleavage by TCRB. Mapping of resistance to UL56 supports and extends recent work showing that UL56 codes for a packaging motif binding protein which also has specific nuclease activity (E. Bogner et al., J. Virol. 72:2259–2264, 1998). Resistance which maps to two different genes suggests that their putative proteins interact and/or that either or both have a benzimidazole ribonucleoside binding site. The results also suggest that the gene products of UL89 and UL56 may be antiviral drug targets.Human cytomegalovirus (HCMV) can cause significant morbidity and mortality in immunocompromised populations (3). It is a common opportunistic disease in patients with AIDS and is often a factor in their death (38). HCMV infection has been implicated in increased risk of organ rejection following heart (28) and kidney transplants (8) and in restenosis of diseased arteries following angioplasty (41, 63). It is also a leading cause of birth defects (16).Current therapies for HCMV infection include ganciclovir (GCV) (22), cidofovir (30), and foscarnet (20). Each of these drugs has several limitations to its use: none are orally bioavailable, all have dose-limiting toxicity, and resistance has developed to each (26). Because all three of these drugs inhibit viral replication through an interaction with the virally encoded DNA polymerase (25, 31, 37), the possibility of cross-resistance exists. Thus, additional drugs with unique mechanisms of action are needed for the treatment of HCMV infections.In 1995, we reported that 2-bromo-5,6-dichloro-1-(β-d-ribofuranosyl)benzimidazole (BDCRB; Fig. ​Fig.1)1) and the 2-chloro analog [2,5,6-trichloro-1-(β-d-ribofuranosyl)benzimidazole TCRB] are potent and selective inhibitors of HCMV replication (55). These compounds have a novel mechanism of action, which unlike the current therapies for HCMV infection, does not involve inhibition of DNA synthesis. The benzimidazole ribonucleosides prevent the cleavage of high-molecular-weight viral DNA concatemers to monomeric genomic lengths (57). Resistance to BDCRB has been mapped to the HCMV UL89 open reading frame (ORF), which, by analogy to gene gp17 from bacteriophage T4, may be a terminase (23, 57). Consequently, we have proposed that the benzimidazole ribonucleosides inhibit the product of this gene and that the UL89 gene product is involved in the viral DNA concatemer cleavage process (57). Open in a separate windowFIG. 1Structure of benzimidazole ribonucleosides. TCRB, R = Cl; BDCRB, R = Br.HCMV replication proceeds in a manner which is conserved among herpesviruses. The virally encoded DNA polymerase produces large, complex head-to-tail concatemers (10, 29, 33) which must be cleaved into genomic-length pieces before insertion into preformed capsids (59). With herpes simplex virus type 1 (HSV-1), temperature-sensitive mutants which are unable to cleave and package the concatemeric DNA have been derived (1, 2, 4, 45, 49, 50, 61). By this process, six HSV-1 genes have been found to be involved in concatemer cleavage and packaging. They are UL6, UL15, UL25, UL28, UL32, and UL33. In addition, recent studies in Homa’s laboratory have established that the product of UL25 is required for viral DNA encapsidation but not cleavage (39). Homologs of these genes exist in HCMV and are UL104, UL89, UL77, UL56, UL52, and UL51, respectively (18).In our continuing investigation of the mode of action of benzimidazole nucleosides, we report herein the independent isolation of HCMV strains resistant to TCRB, characterization of these strains, and identification of the mutations responsible for the development of resistance. The results demonstrate that the mechanism of action of the benzimidazole ribonucleosides is more complex than previously proposed and that a second gene product implicated in DNA cleavage and packaging is involved.     

A Simple and Effective Cleavable Linker for Chemical Proteomics Applications

The study of metabolically labeled or probe-modified proteins is an important area in chemical proteomics. Isolation and purification of the protein targets is a necessary step before MS identification. The biotin-streptavidin system is widely used in this process, but the harsh denaturing conditions also release natively biotinylated proteins and non-selectively bound proteins. A cleavable linker strategy is a promising approach for solving this problem. Though several cleavable linkers have been developed and tested, an efficient, easily synthesized, and inexpensive cleavable linker is a desirable addition to the proteomics toolbox. Here, we describe the chemical proteomics application of a vicinal diol cleavable linker. Through easy-to-handle chemistry we incorporate this linker into an activity-based probe and a biotin alkyne tag amenable for bioorthogonal ligation. With these reagents, background protein identifications are significantly reduced relative to standard on-bead digestion.The covalent modification of proteins by small molecules within a complex proteome is a major theme in chemical biology and proteomics. An effective method for the detection of posttranslational modifications of proteins is the metabolic incorporation of modified biomolecules such as tagged carbohydrates or lipids (1). Reversible interactions of enzyme inhibitors, natural products, or drugs can be detected when one appends photocrosslinking agents, thereby facilitating target discovery (2, 3). A particularly interesting example of protein labeling is activity-based protein profiling (ABPP)¹ (4, 5), which utilizes the intrinsic catalytic activity of a target enzyme for the covalent attachment of an affinity or visualization tag. ABPP makes use of small molecules (activity-based probes (ABPs)) that react with the active form of a specific enzyme or enzyme class by means of a “warhead,” which is often derived from a mechanism-based enzyme inhibitor (Fig. 1A). DCG-04, for example, is based on the naturally occurring inhibitor E-64 and targets the papain family of cysteine proteases via covalent attachment of the epoxysuccinate group to the active site cysteine (Fig. 1B) (6).Open in a separate windowFig. 1.The cleavable linker strategy in ABPP. A, the elements of an ABP. B, the example ABP DCG-04, an epoxysuccinate-containing probe for clan CA cysteine proteases. DCG-04 is based on the naturally occurring protease inhibitor E-64. C, schematic strategy of cleavable linker-mediated target identification. D, the cleavage mechanism of a vicinal diol.Bulky fluorophore or biotin tags on chemical probes might interfere with efficient protein binding. Moreover, they can negatively influence the cell permeability of probes, which therefore limits their applicability in in vitro experiments. Bioorthogonal chemistries, such as the Bertozzi-Staudinger ligation (7) and the 1,3-bipolar cycloaddition of an azide and an alkyne (click chemistry) (8), allow tandem labeling strategies in which a biotin or a fluorophore is attached to an enzyme probe complex in a separate step. Consequently, the probes themselves only carry azide or alkyne groups as “mini-tags.” Tandem labeling using bioorthogonal chemistry has now become a widely used strategy to label biomolecules in lysates and in live cells (9–11).An essential step in ABPP, as well as in other chemical proteomics approaches, is the elucidation of the tagged proteins. This usually involves a biotin-mediated enrichment step followed by mass-spectrometry-based identification. Although the streptavidin-biotin interaction allows efficient enrichment as a result of the strong binding affinity (K_d ∼ 10⁻¹⁵ m), it also has limitations. The quantitative elution of biotinylated proteins requires harsh conditions (12), which lead to contamination of the sample by endogenous biotinylated and non-specifically bound proteins. These other proteins will be identified together with the real protein targets. Given that subsequent target validation with secondary assays can be a costly and time-consuming process, a reduction in false positive identifications is highly desirable. For cleaner protein identification, cleavable linker strategies (13) that allow the selective release of target proteins have been developed (Fig. 1C). The commercially available disulfide linker can be cleaved under mild conditions, but it suffers from premature cleavage in reducing media such as the intracellular environment and reducing buffers used for click chemistry and in vitro reactions of cysteine proteases. Therefore, a variety of alternative linkers for proteomics applications have been reported, including a sterically hindered disulfide (14), diazobenzenes (15–19), hydrazones (20, 21), silanes (22), light sensitive linkers (23–25), tobacco etch virus protease sensitive linkers (26, 27), and a levulinoyl-based linker (28). The synthesis of some of these linkers is lengthy or difficult to scale up, which limits their general application in chemical proteomics.Ideally, a cleavable linker is stable under a wide variety of conditions, is efficiently and selectively cleaved, and can be synthesized in a low number of easy chemical transformations. We aimed to meet these requirements by using a vicinal diol as a cleavable linker system. When vicinal diols are treated with sodium periodate (NaIO₄), the carbon–carbon bond is cleaved (Fig. 1D). Periodate treatment of proteins can result in side-reactions, such as the cleavage of linked carbohydrates or the oxidation of N-terminal serine and threonine residues. However, these N-termini rarely occur in proteins and are therefore of minor concern. In general, the mild, neutral conditions of periodate cleavage are compatible with proteins. This has been illustrated in the past, for example, by its application in the detection of protein–protein interactions (29) and the creation of unliganded MHC class I molecules (30). In this article, we report the chemical proteomics application of diol cleavable linker probes. We show that the synthesis of the linker and its probe derivatives is straightforward, that the linker is compatible with tandem click labeling, that enrichment and release of probe targets is efficient, and that the identification of targets takes place with significantly lower background than in on-bead digestion protocols.     

Generation and Properties of a Streptococcus pneumoniae Mutant Which Does Not Require Choline or Analogs for Growth

A mutant (JY2190) of Streptococcus pneumoniae Rx1 which had acquired the ability to grow in the absence of choline and analogs was isolated. Lipoteichoic acid (LTA) and wall teichoic acid (TA) isolated from the mutant were free of phosphocholine and other phosphorylated amino alcohols. Both polymers showed an unaltered chain structure and, in the case of LTA, an unchanged glycolipid anchor. The cell wall composition was also not altered except that, due to the lack of phosphocholine, the phosphate content of cell walls was half that of the parent strain. Isolated cell walls of the mutant were resistant to hydrolysis by pneumococcal autolysin (N-acetylmuramyl-l-alanine amidase) but were cleaved by the muramidases CPL and cellosyl. The lack of active autolysin in the mutant cells became apparent by impaired cell separation at the end of cell division and by resistance against stationary-phase and penicillin-induced lysis. As a result of the absence of choline in the LTA, pneumococcal surface protein A (PspA) was no longer retained on the cytoplasmic membrane. During growth in the presence of choline, which was incorporated as phosphocholine into LTA and TA, the mutant cells separated normally, did not release PspA, and became penicillin sensitive. However, even under these conditions, they did not lyse in the stationary phase, and they showed poor reactivity with antibody to phosphocholine and an increased release of C-polysaccharide from the cell. In contrast to ethanolamine-grown parent cells (A. Tomasz, Proc. Natl. Acad. Sci. USA 59:86–93, 1968), the choline-free mutant cells retained the capability to undergo genetic transformation but, compared to Rx1, with lower frequency and at an earlier stage of growth. The properties of the mutant could be transferred to the parent strain by DNA of the mutant.Pneumococci differ from other gram-positive bacteria in that their lipoteichoic acid (LTA) and wall teichoic acid (TA) have the same chain structure which is, moreover, unusually complex (Fig. ​(Fig.1):1): glycerophosphate is replaced by ribitol phosphate (7), and between the ribitol phosphate residues a tetrasaccharide is intercalated (23). It contains d-glucose, 2-acetamido-4-amino-2,4,6-trideoxy-d-galactose (AATGal), and two N-acetyl-d-galactosaminyl residues, one or both of which carry a phosphocholine residue at O-6 (references 3 and 12 and this report). Open in a separate windowFIG. 1Pneumococcal TA and LTA. As shown, in strain R6 most of the repeats carry two phosphocholine residues each, at O-6 of the N-acetyl-d-galactosaminyl residues (3, 12). In strain Rx1 and Rx1/AL⁻, most repeats contain one phosphocholine residue (this report) attached to O-6 of the non-ribitol-linked galactosaminyl residue (14).Pneumococci are not able to synthesize the choline required for the synthesis of these substituents. Moreover, choline is an essential growth factor (2, 30) but can be substituted in this function by nutritional ethanolamine (EA) (38). Phosphoethanolamine is incorporated into LTA and TA in place of phosphocholine (14), but it cannot replace phosphocholine functionally. Phosphocholine-substituted LTA serves to anchor pneumococcal surface protein A (PspA) to the outer layer of the cytoplasmic membrane, with choline-mediated interaction between membrane-associated LTA and the C-terminal repeat region of PspA. In EA-grown bacteria, PspA is no longer retained and is released into the surrounding medium (45). Phosphocholine substituents also play an essential role for the activity of the major pneumococcal autolysin, an N-acetylmuramyl-l-alanine amidase (38). This protein possesses a choline-binding C-terminal domain that is essential for activity but, unlike PspA, is not essential for retention on the pneumococcal cell surface (16, 32). Binding of phosphocholine-substituted LTA to this domain results in potent inhibition of the amidase (21). The inhibitory property is dependent on the micellar structure of LTA (13) and lost by deacylation (5). Phosphocholine-substituted LTA may also participate in the transport of the amidase through the cytoplasmic membrane from the cytosol (5), the location of its synthesis (15). It additionally effects the conversion of the inactive E form of the enzyme into the active C form (5). This conversion is likewise effected by the choline residues of cell wall-linked TA (33, 39). Furthermore, binding of the amidase to the choline residues of TA is prerequisite for the hydrolysis of cell walls by the enzyme (18, 22). It should be noted that the amidase is not essential for growth. Though the enzyme is completely inactive in EA grown cells, the growth rate is not affected. However, cell separation is impaired, and there is a loss of stationary-phase and penicillin-induced cell lysis (38, 40), as well as a loss of genetic transformation (38). After insertional inactivation of the autolysin gene (lytA), the autolysin-deficient mutants (Lyt⁻) grew normally (31) and did not even show impeded cell separation (41).In this report, we describe a mutant which acquired the ability to grow in the absence of choline and analogs. Except for the observation that [³H]choline-substituted LTA is not a precursor of [³H]choline-substituted TA (6), nothing is known about the biosyntheses of pneumococcal LTA and TA and the stage of biosynthesis at which phosphocholine is incorporated. Since the absence of choline incorporation might affect the structure of LTA and TA as well as the composition of cell walls, we included relevant analyses in our study.(A preliminary report of this work was presented in an overview on pneumococcal LTA and TA at the International Meeting on the Molecular Biology of Streptococcus pneumoniae and Its Diseases, Oeiras, Portugal, September 24 to 29, 1996 [10].)     

FANCI Protein Binds to DNA and Interacts with FANCD2 to Recognize Branched Structures

In this study, we report that the purified wild-type FANCI (Fanconi anemia complementation group I) protein directly binds to a variety of DNA substrates. The DNA binding domain roughly encompasses residues 200–1000, as suggested by the truncation study. When co-expressed in insect cells, a small fraction of FANCI forms a stable complex with FANCD2 (Fanconi anemia complementation group D2). Intriguingly, the purified FANCI-FANCD2 complex preferentially binds to the branched DNA structures when compared with either FANCI or FANCD2 alone. Co-immunoprecipitation with purified proteins indicates that FANCI interacts with FANCD2 through its C-terminal amino acid 1001–1328 fragment. Although the C terminus of FANCI is dispensable for direct DNA binding, it seems to be involved in the regulation of DNA binding activity. This notion is further enhanced by two C-terminal point mutations, R1285Q and D1301A, which showed differentiated DNA binding activity. We also demonstrate that FANCI forms discrete nuclear foci in HeLa cells in the absence or presence of exogenous DNA damage. The FANCI foci are colocalized perfectly with FANCD2 and partially with proliferating cell nuclear antigen irrespective of mitomycin C treatment. An increased number of FANCI foci form and become resistant to Triton X extraction in response to mitomycin C treatment. Our data suggest that the FANCI-FANCD2 complex may participate in repair of damaged replication forks through its preferential recognition of branched structures.Fanconi anemia (FA)³ is a genetic disorder characterized by chromosome instability, predisposition to cancer, hypersensitivity to DNA cross-linking agents, developmental abnormalities, and bone marrow failure (1–9). There are at least 13 distinct FA complementation groups, each of which is associated with an identified gene (2, 9, 10). Eight of them are components of the FA core complex (FANC A, B, C, E, F, G, L, and M) that is epistatic to the monoubiquitination of both FANCI and FANCD2, a key event to initiate interstrand cross-link (ICL) repair (2, 9, 11). Downstream of or parallel to the FANCI and FANCD2 monoubiquitination are the proteins involved in double strand break repair and breast cancer susceptibility (i.e. FANCD1/BRCA2, FANCJ/BRIP1, and FANCN/PALB2) (2, 9).FANCI is the most recently identified FA gene (11–13). FANCI protein is believed to form a FANCI-FANCD2 (ID) complex with FANCD2, because they co-immunoprecipitate with each other from cell lysates and their stabilities are interdependent of each other (9, 11, 13). FANCI and FANCD2 are paralogs to each other, since they share sequence homology and co-evolve in the same species (11). Both FANCI and FANCD2 can be phosphorylated by ATR/ATM (ataxia telangiectasia and Rad3-related/ataxia telangiectasia-mutated) kinases under genotoxic stress (11, 14, 15). The phosphorylation of FANCI seems to function as a molecular switch to turn on the FA repair pathway (16). The monoubiquitination of FANCD2 at lysine 561 plays a critical role in cellular resistance to DNA cross-linking agents and is required for FANCD2 to form damage-induced foci with BRCA1, BRCA2, RAD51, FANCJ, FANCN, and γ-H2AX on chromatin during S phase of the cell cycle (17–25). In response to DNA damage or replication stress, FANCI is also monoubiquitinated at lysine 523 and recruited to the DNA repair nuclear foci (11, 13). The monoubiquitination of both FANCI and FANCD2 depends on the FA core complex (11, 13, 26), and the ubiquitination of FANCI relies on the FANCD2 monoubiquitination (2, 11). In an in vitro minimally reconstituted system, FANCI enhances FANCD2 monoubiquitination and increases its specificity toward the in vivo ubiquitination site (27).FANCI is a leucine-rich peptide (14.8% of leucine residues) with limited sequence information to indicate which processes it might be involved in. Besides the monoubiquitination site Lys⁵²³ and the putative nuclear localization signals (Fig. 1A), FANCI contains both ARM (armadillo) repeats and a conserved C-terminal EDGE motif as FANCD2 does (11, 28). The EDGE sequence in FANCD2 is not required for monoubiquitination but is required for mitomycin C (MMC) sensitivity (28). The ARM repeats form α-α superhelix folds and are involved in mediating protein-protein interactions (11, 29). In addition, FANCI, at its N terminus, contains a leucine zipper domain (aa 130–151) that could be involved in mediating protein-protein or protein-DNA interactions (Fig. 1A) (30–33). FANCD2, the paralog of FANCI, was reported to bind to double strand DNA ends and Holliday junctions (34).Open in a separate windowFIGURE 1.Purified human FANCI binds to DNA promiscuously. A, schematic diagram of predicted FANCI motifs and mutagenesis strategy to define the DNA binding domain. The ranges of numbers indicate how FANCI was truncated (e.g. 801–1328 represents FANCI-(801–1328)). NLS, predicted nuclear localization signal (aa 779–795 and 1323–1328); K523, lysine 523, the monoubiquitination site. The leucine zipper (orange bars, aa 130–151), ARM repeats (green bars), and EDGE motif (blue bars) are indicated. Red bars with a slash indicate the point mutations shown on the left. B, SDS-PAGE of the purified proteins stained with Coomassie Brilliant Blue R-250. R1285Q and D1301A are two point mutants of FANCI. All FANCI variants are tagged by hexahistidine. FANCD2 is in its native form. Protein markers in kilodaltons are indicated. C, titration of WT-FANCI for the DNA binding activity. Diagrams of the DNA substrates are shown at the top of each set of reactions. *, ³²P-labeled 5′-end. HJ, Holliday junction. Concentrations of FANCI were 0, 20, 40, 60, and 80 nm (ascending triangles). The substrate concentration was 1 nm. Protein-DNA complex is indicated by an arrow. D, supershift assay. 1 nm of ssDNA was incubated with PBS (lane 1), 80 nm FANCI alone (lane 2), and 80 nm FANCI preincubated with a specific FANCI antibody (lane 3) in the condition described under “Experimental Procedures.”In order to delineate the function of FANCI protein, we purified the recombinant FANCI from the baculovirus expression system. In this study, we report the DNA binding activity of FANCI. Unlike FANCD2, FANCI binds to different DNA structures, including single-stranded DNA (ssDNA), double-stranded DNA (dsDNA), 5′-tailed, 3′-tailed, splayed arm, 5′-flap, 3′-flap, static fork, and Holliday junction with preference toward branched structures in the presence of FANCD2. Our data suggest that the dynamic DNA binding activity of FANCI and the preferential recognition of branched structures by the ID complex are likely to be the mechanisms to initiate downstream repair events.