Epsilon-adenylylated glutamine synthetase: an internal fluorescence probe for enzyme conformation

Probing adenylation: using a fluorescently labelled ATP probe to directly label and immunoprecipitate VopS substrates

The bacterial effector VopS from Vibrio parahaemolyticus modifies host Rho GTPases to prevent downstream signalling, which leads to cell rounding and eventually apoptosis. While previous studies have used [α-(32)P] ATP for studying this enzyme, we sought to develop a non-radioactive chemical probe of VopS function. To guide these studies, the kinetic parameters were determined for a variety of nucleotides and the results indicated that the C6 position of adenosine was amenable to modification. Since Fl-ATP is a commercially available ATP analogue that is fluorescently tagged at the C6 position, we tested it as a VopS substrate, and the results show that VopS uses Fl-ATP to label Cdc42 in vitro and in MCF7 whole cell extracts. The utility of this probe was further demonstrated by immunoprecipitating Fl-ATP labeled Cdc42 as well as several novel substrate proteins. The proteins, which were identified by LC-MS/MS, include the small GTPases Rac1 and Cdc42 as well as several proteins that are potential VopS substrates and may be important for V. parahaemolyticus pathology. In total, these studies identify Fl-ATP as a valuable chemical probe of protein AMPylation.

A chemical reporter for protein AMPylation

Protein AMPylation is an emerging post-translational modification, which plays key roles in bacterial pathogenesis and cell biology. Enzymes with AMPylation activity, referred to as AMPylators, have been identified in several bacterial pathogens and eukaryotes. To facilitate the study of this unique modification, we developed an alkynyl chemical reporter for detection and identification of protein AMPylation substrates. Covalent functionalization of AMPylation substrates with the alkynyl reporter in lieu of adenylyl 5'-monophosphate (AMP) allows their subsequent bioorthogonal ligation with azide-fluorescent dyes or affinity enrichment tags. We show that this chemical reporter is transferred by a range of AMPylators onto their cognate protein substrates and allows rapid detection and identification of AMPylated substrates.

Spectroscopic sensitivity of linear-benzoadenine nucleotides to divalent metal counterions, side chain conformations, micelles, and enzymes

From pK(a) data for lin-benzoadenosine 5'-mono-, 5'-di-, and 5'-triphosphates, which are fluorescent "stretched-out" analogues of adenine nucleotides, it was possible to designate the cases of interaction of phosphate with the heteroaromatic moiety. The addition of divalent metal cations or quaternary ammonium micelles diminishes the direct intramolecular interaction between the phosphate(s) and base and consequently brings the pK(a) values close to that of lin-benzoadenosine. Fluorescence spectroscopy was used to investigate the interaction of lin-benzoadenine nucleotides with Mg(2+), Mn(2+), and Co(2+). The association constants for the formation of such complexes were obtained from measurements of steady-state fluorescence quenching. Phase and modulation measurements of the fluorescence lifetimes of lin-benzoadenine nucleotides as a function of Co(2+) concentration permitted determination of the static component of the quenching due to intramolecular complex formation. The association constants of the lin-benzoadenine nucleotides with all of the divalent metal ions studied were greater than those observed for the corresponding adenine nucleotides and were in the order: lin-benzo-ATP > lin-benzo-ADP > lin-benzo-AMP. Fourier transform (1)H NMR of lin-benzo-ATP in the presence of Co(2+) showed broadening of the aromatic proton signals, the 2-H signal (corresponding to the 8-H in ATP) being the most affected. Models are proposed to explain the phosphate-base interaction, the influence of metal ions on base protonation, and the intramo- the intramolecular quenching observed in the complexes due to paramagnetic ion (Co(2+), Mn(2+)) and base interaction.

Time-resolved fluorescence and computational studies of adenylylated glutamine synthetase: analysis of intersubunit interactions

Adenylylation of Tyr-397 of each subunit of Escherichia coli glutamine synthetase (GS) down-regulates enzymatic activity in vivo. The overall structure of the enzyme consists of 12 subunits arranged as two hexamers, face to face. Research reported in this paper addresses the question of whether the covalently attached adenylyl group interacts with neighboring amino acid residues to produce the regulatory phenomenon. Wild-type GS has two Trp residues (positions 57 and 158) and the adenylylation site lies within 7-8 A of the Trp-57 loop in the adjacent subunit of the same hexameric ring; Trp-158 is about 35 A from the site of adenylylation. Fluorescence lifetimes and quantum yields have been determined for two fluorophores with wild-type and mutant GS. One fluorophore is epsilon-AMP adenylylated GS (at Tyr-397), and the other fluorophore is the intrinsic protein residue Trp-57. These experiments were conducted in order to detect possible intersubunit interactions between adenylyl groups and the neighboring Trp-57 to search for a role for the Trp-57 loop in the regulation of GS. The fluorescence due to epsilon-AMP of two adenylylated enzymes, wild-type GS and the W158F mutant, exhibits heterogeneous decay kinetics; the data adequately fit to a double exponential decay model with recovered average lifetime values of 18.2 and 2.1 ns, respectively. The pre-exponential factors range from 0.66 to 0.73 for the long lifetime component, at five emission wavelengths. The W57L-epsilon-AMP enzyme yields longer average lifetime values of 19.5 and 2.4 ns, and the pre-exponential factors range from 0.82 to 0.85 for the long lifetime component. An additional residue in the Trp-57 loop, Lys-58, has been altered and the K58C mutant enzyme has been adenylylated with epsilon-AMP on Tyr-397. Lys-58 is near the ATP binding site and may represent a link by which the adenylyl group controls the activity of GS. The fluorescence of epsilon-AMP-adenylylated K58C mutant GS is best described by a triple exponential decay with average recovered lifetime values of 19.9, 4.6, and 0.58 ns, with the largest fraction being the median lifetime component. Relative quantum yields of epsilon-AMP-Tyr-397 were measured in order to determine if static quenching occurs from adenine-indole stacking in the wild-type GS. The relative quantum yield of the epsilon-AMP-adenylylated W57L mutant is larger than the wild-type protein by the amount predicted from the difference in lifetime values: thus, no static quenching is evident.(ABSTRACT TRUNCATED AT 400 WORDS)

Relation between the adenylylation state of glutamine synthetase and the expression of other genes involved in nitrogen metabolism

We have partially characterized the biochemical parameters of glutamine synthetase from Klebsiella pneumoniae and have shown that the differential affinity of adenylylated and unadenylylated glutamine synthetase for adenosine diphosphate provides a convenient means of determining the adenylylation state. Using this assay procedure, we examined the relationship between the adenylylation state and the expression of other genes involved in nitrogen assimilation. We observed no correlation between the adenylylation state and the expression of histidase, glutamine synthetase, glutamate synthase, glutamate dehydrogenase, and urease in aerobic cultures.

Topographical analysis of regulatory and metal ion binding sites on glutamine synthetase from Escherichia coli: 13C and 31P nuclear magnetic resonance and fluorescence energy transfer study

The paramagnetic effect of Mn(II) on (13)C and (31)P nuclear magnetic resonance signals from the [2-(13)C]ATP adenylylated glutamine synthetase [L-glutamate:ammonia ligase (ADP-forming); EC 6.3.1.2] from Escherichia coli was measured. This effect permitted the determination of distances from the 2-C position and the phosphorus of covalently bound AMP to the two Mn(II) binding sites, n(1) and n(2). Binding of Mn(II) to the n(1) site converts an inactive apo-enzyme to its active form, while the metal ion bound at n(2) occupies the metal-nucleotide substrate site. The distances from Mn(II) at the n(1) and n(2) sites to phosphorus are approximately 10 and approximately 7 A and to the 2-C position of the adenine ring are approximately 12 and approximately 11 A, respectively. The fluorescence energy transfer method was used to determine distances between Co(II) at n(1) and n(2) and the adenylyl site. For this experiment the enzyme was adenylylated with epsilon-ATP. The distances between epsilon-adenine and Co(II) at n(1) and n(2) are approximately 13 and approximately 11 A, respectively. Quantitation of the paramagnetic effect due to Co(II) on the (31)P nuclear magnetic resonance signal yielded values of 8 and 6 A for the distances between the phosphorus of the covalently bound AMP and the n(1) and n(2) sites, respectively. The results reveal that the covalent modification site is very close to the catalytic center of the enzyme. In this study both nuclear magnetic resonance and fluorescence energy transfer techniques have been used to determine distances between the same set of sites on an enzyme surface.