ADP-ribosylation of Rhizobium meliloti glutamine synthetase III in vivo

Endogenous protein mono-ADP-ribosylation in Arabidopsis thaliana

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.

Analysis and identification of ADP-ribosylated proteins of Streptomyces coelicolor M145

Mono-ADP-ribosylation is the enzymatic transfer of ADP-ribose from NAD(+) to acceptor proteins catalyzed by ADP-ribosyltransferases. Using m-aminophenylboronate affinity chromatography, 2D-gel electrophoresis, in-gel digestion and MALDI-TOF analysis we have identified eight in vitro ADP-ribosylated proteins in Streptomyces coelicolor, which can be classified into three categories: (i) secreted proteins; (ii) metabolic enzymes using NAD(+)/NADH or NADP(+)/NADPH as coenzymes; and (iii) other proteins. The secreted proteins could be classified into two functional categories: SCO2008 and SC05477 encode members of the family of periplasmic extracellular solute-binding proteins, and SCO6108 and SC01968 are secreted hydrolases. Dehydrogenases are encoded by SC04824 and SC04771. The other targets are GlnA (glutamine synthetase I., SC02198) and SpaA (starvation-sensing protein encoded by SC07629). SCO2008 protein and GlnA had been identified as ADP-ribosylated proteins in previous studies. With these results we provided experimental support for a previous suggestion that ADP-ribosylation may regulate membrane transport and localization of periplasmic proteins. Since ADP-ribosylation results in inactivation of the target protein, ADP-ribosylation of dehydrogenases might modulate crucial primary metabolic pathways in Streptomyces. Several of the proteins identified here could provide a strong connection between protein ADP-ribosylation and the regulation of morphological differentiation in S. coelicolor.

Lengsin is a survivor of an ancient family of class I glutamine synthetases re-engineered by evolution for a role in the vertebrate lens

Lengsin is a major protein of the vertebrate eye lens. It belongs to the hitherto purely prokaryotic GS I branch of the glutamine synthetase (GS) superfamily, but has no enzyme activity. Like the taxon-specific crystallins, Lengsin is the result of the recruitment of an ancient enzyme to a noncatalytic role in the vertebrate lens. Cryo-EM and modeling studies of Lengsin show a dodecamer structure with important similarities and differences with prokaryotic GS I structures. GS homology regions of Lengsin are well conserved, but the N-terminal domain shows evidence of dynamic evolutionary changes. Compared with birds and fish, most mammals have an additional exon corresponding to part of the N-terminal domain; however, in human, this is a nonfunctional pseudoexon. Genes related to Lengsin are also present in the sea urchin, suggesting that this branch of the GS I family, supplanted by GS II enzymes in vertebrates, has an ancient role in metazoans.

Distinct roles of P(II)-like signal transmitter proteins and amtB in regulation of nif gene expression, nitrogenase activity, and posttranslational modification of NifH in Azoarcus sp. strain BH72

P(II)-like signal transmitter proteins, found in Bacteria, Archaea, and plants, are known to mediate control of carbon and nitrogen assimilation. They indirectly regulate the activity of key metabolic enzymes and transcription factors by protein-protein interactions with signal transduction proteins. Many Proteobacteria harbor two paralogous P(II)-like proteins, GlnB and GlnK, whereas a novel third P(II) paralogue (GlnY) was recently identified in Azoarcus sp. strain BH72, a diazotrophic endophyte of grasses. In the present study, evidence was obtained that the P(II)-like proteins have distinct roles in mediating nitrogen and oxygen control of nif gene transcription and nitrogenase activity. Full repression of nif gene transcription in the presence of a combined nitrogen source or high oxygen concentrations was observed in wild-type and glnB and glnK knockout mutants, revealing that GlnB and GlnK can complement each other in mediating the repression. In contrast, in a glnBK double mutant strain in the presence of only GlnY, nif gene transcription was still detectable, albeit at a lower level, on nitrate or 20% oxygen. As another level of control, nitrogenase activity was regulated by at least three types of mechanisms in strain BH72: covalent modification of dinitrogenase reductase (NifH), probably by ADP-ribosylation, and two other, unknown means. Functional inactivation upon ammonium addition (switch-off) required the putative high-affinity ammonium transporter AmtB and GlnK, but not GlnB or GlnY. Functional inactivation in response to anaerobiosis did not depend on AmtB, GlnK, or GlnB. In contrast, covalent modification of NifH required both GlnB and GlnK and AmtB as response to ammonium addition, whereas it required either GlnB or GlnK and not AmtB when cells were shifted to anaerobiosis. In a glnBK double mutant expressing only GlnY, NifH modification was completely abolished, further revealing functional differences between the three P(II) paralogues.

Induced mono-(ADP)-ribosylation of rat liver cytosolic proteins by lipid peroxidant agents

We have studied the effect of free radical generating agents on the mono-(ADP)-ribosylation of rat liver cytosolic proteins. Our results show that this post-translational modification, whose physiological significance is still unclear, is activated by lipid peroxidant agents via activation of cytoplasmatic mono-(ADP)-ribosyltransferases. The implication of free radicals in this process is demonstrated by the fact that mono-(ADP)-ribosylation can be prevented by melatonin, N-tert-butyl-alpha-phenylnitrone and dithiothreitol. On the basis of our results, we discuss the modification of proteins caused by free radicals as a possible mechanism by which they damage the cell.

Function and regulation of glnA in the methanogenic archaeon Methanococcus maripaludis

The glnA gene in the domains Bacteria and Archaea encodes glutamine synthetase, a universally distributed enzyme that functions in ammonia assimilation and glutamine synthesis. We investigated the regulation and function of glnA in the methanogenic archaeon Methanococcus maripaludis. The deduced amino acid sequence of the gene demonstrated its membership in class GSI-alpha of glutamine synthetases. The gene appeared to be expressed as a monocistronic operon. glnA mRNA levels and specific activities of glutamine synthetase were regulated similarly by nitrogen. Three transcription start sites were identified, corresponding to two overlapping nitrogen-regulated promoters and one weaker constitutive promoter. An inverted repeat immediately upstream of the regulated transcription start sites mediated repression under noninducing conditions. Thus, mutations that altered the sequence of the inverted repeat resulted in derepression. The inverted repeat had sequence similarity with a repeat that we previously identified as the nif operator of M. maripaludis, suggesting a common mechanism of nitrogen regulation. Efforts to produce a glnA null mutant failed, suggesting that glnA is an essential gene in M. maripaludis.

Uridylylation of the P(II) protein in the photosynthetic bacterium Rhodospirillum rubrum

The regulatory protein P(II) has been studied in great detail in enteric bacteria; however, its function in photosynthetic bacteria has not been clearly established. As a number of these bacteria have been shown to regulate nitrogenase activity by a metabolic control system, it is of special interest to establish the role of P(II) in these diazotrophs. In this study, we show that P(II) in Rhodospirillum rubrum is modified in response to the N status in the cell and that addition of ammonium or glutamine leads to demodification. We also provide evidence that P(II) is uridylylated. In addition, we show that not only these compounds but also NAD+ promotes demodification of P(II), which is of particular interest as this pyridine nucleotide has been shown to act as a switch-off effector of nitrogenase. Demodification of P(II) by ammonium or NAD+ did not occur in cultures treated with an inhibitor of glutamine synthetase (methionine sulfoximine), whereas treatment with the glutamate synthase inhibitor 6-diazo-5-oxo-norleucine led to total demodification of P(II) without any other addition. The results indicate that P(II) probably is not directly involved in darkness switch-off of nitrogenase but that a role in ammonium switch-off cannot be excluded.

Endogenous ADP-ribosylation of proteins in Mycobacterium smegmatis

Endogenous ADP-ribosylation of two proteins with molecular weights of 30,000 (30K) and 80,000 (80K) was detected in cell extracts of Mycobacterium smegmatis. Modification of these proteins was enzymatic. The ADP-ribose bound to 30K was removed by HgCl2 but not by NH2OH, suggesting the modification of a cysteine residue. The ADP-ribose bound to 80K was not removed by either HgCl2 or NH2OH, which is consistent with the modification of an asparagine residue. ADP-ribosylation of 80K appeared to be reversible.

ADP-ribosylation of an approximately 70-kilodalton protein of Klebsiella pneumoniae

An approximately 70-kDa protein in the culture supernatant of a human pathogenic strain of Klebsiella pneumoniae was labeled in the presence of [32P-adenylate]NAD. Labeling was significantly increased by the addition of dithiothreitol ( > 1 mM) but prevented by treatment of the culture supernatant for 3 min at 56 degrees C. The addition of unlabeled NAD, but not of ADP-ribose, blocked labeling of the approximately 70-kDa protein. The radioactive label was released by formic acid but not by HgCl2 (1 mM) or neutral hydroxylamine (0.5 M). The addition of homogenates of human platelets, human neutrophils, rat brain, rat lung, or rat spleen tissues to the culture supernatant did not induce labeling of eukaryotic proteins. The data indicate that the K. pneumoniae strain produces ADP-ribosyltransferase which modifies an endogenous protein.

Mono-ADP-ribosylation: a reversible posttranslational modification of proteins

Mono-ADP-ribosyltransferase activity has been detected in numerous vertebrate tissues and transferase cDNAs from a few species have recently been cloned. In vitro ADP-ribosylation has been demonstrated with diverse substrates such as phosphorylase kinase, actin, and Gs alpha resulting in the alteration of substrate function. ADP-ribosylation of endogenous target proteins has been observed in chicken heterophils, rat brain, and human platelets, and integrin alpha 7 was found to be the endogenous substrate of the GPI-anchored rabbit skeletal muscle transferase. The reversibility of ADP-ribosylation is made possible by ADP-ribosylarginine hydrolases which have been isolated and cloned from rodent and human tissues. The transferases and hydrolases could in principle form an intracellular ADP-ribosylation regulatory cycle. In the case of the skeletal muscle transferases, however, processing of ADP-ribosylated integrin alpha 7 is carried out by phosphodiesterases and possibly phosphatases (Fig. 1). Most bacterial toxin and eukaryotic mono-ADP-ribosyltransferases, and perhaps other NAD-utilizing enzymes such as the RT6 family of proteins, share a common catalytic-site structure despite a lack of overall sequence identity. The transferases that have been studied thus far possess a critical glutamic acid and other amino acids at the catalytic cleft which function to position NAD for nucleophilic attack at the N-glycosidic linkage for either ADP-ribose transfer or NAD hydrolysis. The amino acid differences among transferases at the active site may reflect different catalytic mechanisms of ADP-ribosylation or may be required for accommodating the different ADP-ribose acceptor molecules.

Structure and function of eukaryotic mono-ADP-ribosyltransferases

ADP-ribosylation of proteins has been observed in numerous animal tissues including chicken heterophils, rat brain, human platelets, and mouse skeletal muscle. ADP-ribosylation in these tissues is thought to modulate critical cellular functions such as muscle cell development, actin polymerization, and cytotoxic T lymphocyte proliferation. Specific substrates of the ADP-ribosyltransferases have been identified; the skeletal muscle transferase ADP-ribosylates integrin alpha 7 whereas the chicken heterophil enzyme modifies the heterophil granule protein p33 and the CTL enzyme ADP-ribosylates the membrane-associated protein p40. Transferase sequence has been determined which should assist in elucidating the role of ADP-ribosylation in cells. There is sequence similarity among the vertebrate transferases and the rodent RT6 alloantigens. The RT6 family of proteins are NAD glycohydrolases that have been shown to possess auto-ADP-ribosyltransferase activity whereas the mouse Rt6-1 is also capable of ADP-ribosylating histone. Absence of RT6+ T cells has been associated with the development of an autoimmune-mediated diabetes in rodents. Humans have an RT6 pseudogene and do not express RT6 proteins. The reversal of ADP-ribosylation is catalyzed by ADP-ribosylarginine hydrolases, which have been purified and cloned from rodent and human tissues. In principle, the transferases and hydrolases could form an intracellular ADP-ribosylation regulatory cycle. In skeletal muscle and lymphocytes, however, the transferases and their substrates are extracellular membrane proteins whereas the hydrolases described thus far are cytoplasmic. In cultured mouse skeletal muscle cells, processing of the ADP-ribosylated integrin alpha 7 was carried out by phosphodiesterases and possibly phosphatases, leaving a residual ribose attached to the (arginine)protein. Several bacterial toxin and eukaryotic mono-ADP-ribosyltransferases, and perhaps other NAD-utilizing enzymes such as the RT6 alloantigens share regions of amino acid sequence similarity, which form, in part, the catalytic site. The catalytic cleft, found in the bacterial toxins that have been studied thus far, contains a critical glutamate and other amino acids that function to position NAD for nucleophilic attack at the N-glycosidic linkage, for either ADP-ribose transfer or NAD hydrolysis. Amino acid differences among the transferases at the active site may be required for accommodating the different ADP-ribose acceptor molecules.

Nitrogen control in bacteria

Nitrogen metabolism in prokaryotes involves the coordinated expression of a large number of enzymes concerned with both utilization of extracellular nitrogen sources and intracellular biosynthesis of nitrogen-containing compounds. The control of this expression is determined by the availability of fixed nitrogen to the cell and is effected by complex regulatory networks involving regulation at both the transcriptional and posttranslational levels. While the most detailed studies to date have been carried out with enteric bacteria, there is a considerable body of evidence to show that the nitrogen regulation (ntr) systems described in the enterics extend to many other genera. Furthermore, as the range of bacteria in which the phenomenon of nitrogen control is examined is being extended, new regulatory mechanisms are also being discovered. In this review, we have attempted to summarize recent research in prokaryotic nitrogen control; to show the ubiquity of the ntr system, at least in gram-negative organisms; and to identify those areas and groups of organisms about which there is much still to learn.

ADP-ribosylation of glutamine synthetase in the cyanobacterium Synechocystis sp. strain PCC 6803

Glutamine synthetase (GS) inactivation was observed in crude cell extracts and in the high-speed supernatant fraction from the cyanobacterium Synechocystis sp. strain PCC 6803 following the addition of ammonium ions, glutamine, or glutamate. Dialysis of the high-speed supernatant resulted in loss of inactivation activity, but this could be restored by the addition of NADH, NADPH, or NADP+ and, to a lesser extent, NAD+, suggesting that inactivation of GS involved ADP-ribosylation. This form of modification was confirmed both by labelling experiments using [32P]NAD+ and by chemical analysis of the hydrolyzed enzyme. Three different forms of GS, exhibiting no activity, biosynthetic activity only, or transferase activity only, could be resolved by chromatography, and the differences in activity were correlated with the extent of the modification. Both biosynthetic and transferase activities were restored to the completely inactive form of GS by treatment with phosphodiesterase.