Isolation and Identification of Novel ADP-Ribosylated Proteins from Streptomyces coelicolor A3(2)

An important role of protein ADP-ribosylation in bacterial morphogenesis has been proposed (J. Bacteriol. 178, 3785-3790; 178, 4935-4941). To clarify the detail of ADP-ribosylation, we identified a new kind of target protein for ADP-ribosylation in Streptomyces coelicolor A3(2) grown to the late growth phase. All four proteins (MalE, BldKB, a periplasmic protein for binding branched-chain amino-acids, and a periplasmic solute binding protein) were functionally similar and participated in the regulation of transport of metabolites or nutrients through the membrane. ADP-ribosylation was likely to occur on a cysteine residue, because the modification group was removed by mercuric chloride treatment. The modification site may be the site of lipoprotein modification necessary for protein export. This report is the first suggesting that certain proteins involved in membrane transport can be ADP-ribosylated.     

Endogenous protein mono-ADP-ribosylation in <Emphasis Type="Italic">Arabidopsis thaliana</Emphasis>

Protein mono-ADP-ribosylation post-translationally transfers the ADP-ribose moiety from the β-NAD⁺ donor to various protein acceptors. This type of modification has been widely characterized and shown to regulate protein activities in animals, yeast and prokaryotes, but has never been reported in plants. In this study, using [³²P]NAD⁺ as the substrate, ADP-ribosylated proteins in Arabidopsis were investigated. One protein substrate of 32 kDa in adult rosette leaves was found to be radiolabeled. Heat treatment, protease sensitivity and nucleotide derivative competition assays suggested a covalent reaction of NAD⁺ with the 32 kDa protein. [carbonyl-¹⁴C]NAD⁺ could not label the 32 kDa protein, confirming that the modification was ADP-ribosylation. Poly (ADP-ribose) polymerase inhibitor failed to suppress the reaction, but chemicals that destroy mono-ADP-ribosylation on specific amino acid residues could break up the linkage, suggesting that the reaction was not a poly-ADP-ribosylation but rather a mono-ADP-ribosylation. This modification mainly existed in leaves and was enhanced by oxidative stresses. In young seedlings, two more protein substrates with the size of 45 kDa and over 130 kDa, respectively, were observed in addition to the 32 kDa protein, indicating that different proteins were modified at different developmental stages. Although the substrate proteins remain to be identified, this is the first report on the characterization of endogenously mono-ADP-ribosylated proteins in plants.     

In vitro ADP-ribosylation of chromosomal proteins of the brain of developing rats

In vitro ADP-ribosylation of chromosomal protein and its modulation by spermine, 3-aminobenzamide (3-AB) and benzamide were studied by incubating the nuclei of cerebral hemisphere of 3-, 14- and 30-day old rats with ³²P-NAD⁺. Histones get ADP-ribosylated more than the non-histone chromosomal (NHC) protein. H1 is the major target for ADP-ribosylation. Among the nucleosomal histones, H2B is ADP-ribosylated most. The other core histones also get ADP-ribosylated to a lesser extent. ADP-ribosylation of both histones and NHC proteins decreases during development. Spermine stimulates, whereas 3-AB and benzamide inhibit, ³²P-ADP-ribose incorporation into histones and NHC proteins. These effects decrease with development. Mild digestion of chromatin by micrococcal nuclease (MNase), EcoRI, and AluI prior to ADP-ribosylation stimulates incorporation of ³²P-ADP-ribose. The degree of stimulation decreases as development proceeds. Such alterations indicate progressive condensation of chromatin with development.     

Sirtuin chemical mechanisms

Sirtuins are ancient proteins widely distributed in all lifeforms of earth. These proteins are universally able to bind NAD⁺, and activate it to effect ADP-ribosylation of cellular nucleophiles. The most commonly observed sirtuin reaction is the ADP-ribosylation of acetyllysine, which leads to NAD⁺-dependent deacetylation. Other types of ADP-ribosylation have also been observed, including protein ADP-ribosylation, NAD⁺ solvolysis and ADP-ribosyltransfer to 5,6-dimethylbenzimidazole, a reaction involved in eubacterial cobalamin biosynthesis. This review broadly surveys the chemistries and chemical mechanisms of these enzymes.     

Vanadate, epidermal growth factor and the stimulation of DNA synthesis

We present here what we believe to be the first report of the stimulation of NAD⁺-dependent ADP-ribosyltransferase activity by a hormone. Isoproterenol stimulated the ADP-ribosylation of RL-PR-C hepatocyte membranes in a concentration-dependent fashion; the effect was abolished by the β-adrenergic antagonist, propranolol. Although hepatocyte plasma membrane ADP-ribosyltransferase and adenylate cyclase activities differed in their sensitivity to isoproterenol, the kinetics of both effects were quite similar. PAGE separation of membrane proteins after ADP-ribosylation from [2,8-³H-adenine]NAD⁺ identified the acceptor for isoproterenol-enhanced ADP-ribosylation as the same 55,000 dalton guanyl nucleotide regulatory protein serving for both endogenous and cholera toxin-stimulated processes in these cells.     

MonoADP-Ribosylation of the NAD+-Dependent Alcohol Dehydrogenase from Entamoeba histolytica

The human parasite Entamoeba histolytica is an amitochondrial protozoan whose metabolism depends on glucose fermentation. Among the metabolic enzymes absolutely required for amoeba growth is the NAD⁺-dependent alcohol dehydrogenase (EhADH2). The polymeric form of EhADH2 was sedimented at 160,000g, and in this fraction we observed [³²P]-labeling of a 96-kDa protein under mono-ADP-ribosylation conditions with [³²P]NAD⁺. The [³²P]-labeled protein had the same molecular weight as the EhADH2 monomer. Because of the importance of monoADP-ribosylation in the regulation of many physiological processes, the aim of this study was to determine whether EhADH2 is ADP-ribosylated, and what would be the consequence of this modification on its alcohol and aldehyde dehydrogenase enzymatic activities. This study describes the ADP-ribosylation of EhADH2. This modification did not have an effect on the enzymatic activities, but it may regulate other functions of EhADH2.     

ADP-Ribosylation of Human Myelin Basic Protein

Abstract: When isolated myelin membranes were ADP-ribosylated by [³²P]NAD⁺ either in the absence of toxin (by the membrane ADP-ribosyltransferase) or in the presence of cholera toxin, the same proteins were ADP-ribosylated in both cases and myelin basic protein (MBP) was the major radioactive product. Therefore, cholera toxin was considered a good model for ADP-ribosylation of myelin proteins. Although purified human MBP migrates as a single band on sodium dodecyl sulfate-polyacrylamide gel electrophoresis with a molecular mass of 20 kDa, the microheterogeneity that is masked under these conditions can be clearly demonstrated on alkaline-urea gels at pH 10.6. At this pH, MBP is resolved into several components that differ one from the other by a single charge (charge isomers). These charge isomers can be resolved on CM52 columns at pH 10.6, and several can be ADP-ribosylated. Component 1 (C-1), the most cationic charge isomer, incorporated 1.79 mol of ADP-ribose/mol of protein. C-2 and C-3 (which differ from C-1 by the loss of one and two positive charges, respectively) incorporated slightly less at 1.67 and 1.63 mol of ADP-ribose/mol of protein, respectively, whereas C-8, the least cationic, incorporated less than 0.11 mol/mol of protein. In the presence of neutral hydroxylamine, the ADP-ribosyl bond was shown to have a half-life of about 80 min, suggesting an N-glycosidic linkage between ADP-ribose and an arginyl residue of the protein. As MBP contains several components that are ADP-ribosylated to different specific activities, the use of MBP, ADP-ribosylated in the natural membrane, to identify the sites involved would yield a mixture of peptides difficult to resolve. Therefore, to identify the sites ADP-ribosylated, an endoproteinase Lys-C digest of C-1 ADP-ribosylated by cholera toxin was prepared. Two radioactive peptides were isolated by reversed-phase HPLC. Amino acid and sequence analyses identified the radioactive peptides as residues 5–13 and 54–58 of the human sequence (sp. act., 0.89 and 0.62 nmol of ADP-ribose/nmol of peptide, respectively). The ADP-ribosylated residues were identified as Arg⁹ and Arg⁵⁴ by automated and manual Edman sequencing. Taken together with our previous observation that MBP binds GTP at a single site, these data suggest that MBP functions as part of a signal transduction system in myelin.     

Demonstration of choleragen-dependent ADP-ribosylation in whole cells and correlation with the activation of adenylate cyclase

3T3C₂ mouse fibroblasts rendered permeable to (α^?32P)NAD⁺ show cholera toxin-dependent labeling of a 45,000 m.w. protein and of a doublet of polypeptides around 52,000 m.w. These same bands are ADP-ribosylated in broken cells. Membranes prepared from pigeon erythrocytes pretreated with choleragen show a decrease in subsequent cholera toxin-specific ADP-ribosylation of a 43,000 m.w. polypeptide. Both whole cell and broken cell adenylate cyclase activation and toxin-specific ADP-ribosylation are reversed specifically by low pH and high concentrations of toxin and nicotinamide in all systems. Thus ADP-ribosylation appears to be relevant to the molecular action of choleragen in whole cells as well as in broken cells.     

Role of NAD+ and ADP-Ribosylation in the Maintenance of the Golgi Structure

We have investigated the role of the ADP- ribosylation induced by brefeldin A (BFA) in the mechanisms controlling the architecture of the Golgi complex. BFA causes the rapid disassembly of this organelle into a network of tubules, prevents the association of coatomer and other proteins to Golgi membranes, and stimulates the ADP-ribosylation of two cytosolic proteins of 38 and 50 kD (GAPDH and BARS-50; De Matteis, M.A., M. DiGirolamo, A. Colanzi, M. Pallas, G. Di Tullio, L.J. McDonald, J. Moss, G. Santini, S. Bannykh, D. Corda, and A. Luini. 1994. Proc. Natl. Acad. Sci. USA. 91:1114–1118; Di Girolamo, M., M.G. Silletta, M.A. De Matteis, A. Braca, A. Colanzi, D. Pawlak, M.M. Rasenick, A. Luini, and D. Corda. 1995. Proc. Natl. Acad. Sci. USA. 92:7065–7069). To study the role of ADP-ribosylation, this reaction was inhibited by depletion of NAD⁺ (the ADP-ribose donor) or by using selective pharmacological blockers in permeabilized cells. In NAD⁺-depleted cells and in the presence of dialized cytosol, BFA detached coat proteins from Golgi membranes with normal potency but failed to alter the organelle's structure. Readdition of NAD⁺ triggered Golgi disassembly by BFA. This effect of NAD⁺ was mimicked by the use of pre–ADP- ribosylated cytosol. The further addition of extracts enriched in native BARS-50 abolished the ability of ADP-ribosylated cytosol to support the effect of BFA. Pharmacological blockers of the BFA-dependent ADP-ribosylation (Weigert, R., A. Colanzi, A. Mironov, R. Buccione, C. Cericola, M.G. Sciulli, G. Santini, S. Flati, A. Fusella, J. Donaldson, M. DiGirolamo, D. Corda, M.A. De Matteis, and A. Luini. 1997. J. Biol. Chem. 272:14200–14207) prevented Golgi disassembly by BFA in permeabilized cells. These inhibitors became inactive in the presence of pre–ADP-ribosylated cytosol, and their activity was rescued by supplementing the cytosol with a native BARS-50–enriched fraction. These results indicate that ADP-ribosylation plays a role in the Golgi disassembling activity of BFA, and suggest that the ADP-ribosylated substrates are components of the machinery controlling the structure of the Golgi apparatus.     

Characterization of Polyphosphate Glucokinase SCO5059 from Streptomyces coelicolor A3(2)

SCO5059, encoded in Streptomyces coelicolor A3(2), was identified as a polyphosphate glucokinase. The K _m values of SCO5059 for glucose and polyphosphate (poly(P)₆) were estimated to be 12 and 4 µM, respectively, and the k _cat value was 0.3 s^?1 at pH 7.7 at 28 °C. SCO5059 homologs are highly conserved among Streptomyces, and can work as polyphosphate glucokinase as well.     

Isolation and identification of novel ADP-ribosylated proteins from Streptomyces coelicolor A3(2)

An important role of protein ADP-ribosylation in bacterial morphogenesis has been proposed (J. Bacteriol. 178, 3785-3790; 178, 4935-4941). To clarify the detail of ADP-ribosylation, we identified a new kind of target protein for ADP-ribosylation in Streptomyces coelicolor A3(2) grown to the late growth phase. All four proteins (MalE, BldKB, a periplasmic protein for binding branched-chain amino-acids, and a periplasmic solute binding protein) were functionally similar and participated in the regulation of transport of metabolites or nutrients through the membrane. ADP-ribosylation was likely to occur on a cysteine residue, because the modification group was removed by mercuric chloride treatment. The modification site may be the site of lipoprotein modification necessary for protein export. This report is the first suggesting that certain proteins involved in membrane transport can be ADP-ribosylated.     

A possible extended family of regulators of sigma factor activity in Streptomyces coelicolor

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

<Emphasis Type="Italic">tdd8</Emphasis>: a TerD domain-encoding gene involved in <Emphasis Type="Italic">Streptomyces coelicolor</Emphasis> differentiation

The Streptomyces coelicolor genome contains 17 TerD domain-encoding genes (tdd genes) of unknown function. The proteins encoded by these genes have been presumed to be involved in tellurite resistance on the basis of their homology with the protein TerD of Serratia marcescens. To elucidate the role of a Tdd protein (Tdd8), both a deletion mutant for the corresponding gene tdd8 (SCO2368) and a recombinant strain over-expressing tdd8 were produced in S. coelicolor M145. The deletion mutant (Δtdd8), like the wild strain, was not resistant to potassium tellurite. The deletion was not lethal but had a marked effect on differentiation. The deletion strain showed more rapid growth in liquid medium and produced long chains of short spores with a dense and non-spherical spore wall on agar plates. The strain over-expressing tdd8 had a growth delay in liquid medium and produced very few spores of irregular shapes and sizes on solid medium. The results of this study demonstrated that Tdd proteins might have a function other than tellurite resistance and this function seems to be of crucial importance for the proper development of the actinomycete S. coelicolor.     

A novel tyrosine-phosphorylated protein inhibiting the growth of Streptomyces cells

Very few of the tyrosine-phosphorylated proteins in Streptomyces have been identified. Here, we identify a tyrosine-phosphorylated protein from Streptomyces coelicolor A3(2), designated as SCO5717. The protein possesses Walker motifs and a tyrosine cluster at the C-terminus. When sco5717 harboring its own promoter was introduced into the S. coelicolor cell, the growth was inhibited. An sco5717-disrupted mutant formed aerial mycelium earlier than the wild-type strain, suggesting that SCO5717 controls the cell growth of S. coelicolor. Although the recombinant SCO5717 showed an ATPase activity, it lacked self-phosphorylation ability, suggesting that SCO5717 is a novel tyrosine-phosphorylated protein, which is distinguishable from bacterial protein tyrosine kinases known so far.     

A 3-aminobenzamide-resistant labeled protein in [P]NAD-labeled cells

A series of proteins are covalently labeled when human lymphocytes are incubated with [³²P]NAD⁺. The majority of this labeling is effectively inhibited when the lymphocytes are coincubated with 3-aminobenzamide, a potent inhibitor of poly(ADP-ribose) polymerase. However, labeling of a 72 000 molecular weight protein was resistant to the inhibitory effect of 3-aminobenzamide. Labeling of this protein from [³²P]NAD⁺ was shown to be Mg²⁺-dependent. The 72 000 molecular weight protein could also be labeled on incubation with [α-³²P]ATP, [γ-³²P]ATP and [³²P]orthophosphate, but not from [³H]NAD⁺ or [¹⁴C]NAD⁺. In the present study, we show that the 72 000 molecular weight protein is not ADP-ribosylated but rather, phosphorylated on incubation with [³²P]NAD⁺. This phosphorylation appears to occur via an Mg²⁺-dependent conversion of NAD⁺ to AMP with the eventual utilization of the α-phosphate for phosphorylation of the 72 000 molecular weight protein.     

Exploration of geosmin synthase from <Emphasis Type="Italic">Streptomyces peucetius</Emphasis> ATCC 27952 by deletion of doxorubicin biosynthetic gene cluster

Thorough investigation of Streptomyces peucetius ATCC 27952 genome revealed a sesquiterpene synthase, named spterp13, which encodes a putative protein of 732 amino acids with significant similarity to S. avermitilis MA-4680 (SAV2163, GeoA) and S. coelicolor A3(2) (SCO6073). The proteins encoded by SAV2163 and SCO6073 produce geosmin in the respective strains. However, the spterp13 gene seemed to be silent in S. peucetius. Deletion of the doxorubicin gene cluster from S. peucetius resulted in increased cell growth rate along with detectable production of geosmin. When we over expressed the spterp13 gene in S. peucetius DM07 under the control of an ermE* promoter, 2.4 ± 0.4-fold enhanced production of geosmin was observed.