Identification of novel proteins secreted by Lactobacillus rhamnosus GG grown in de Mann-Rogosa-Sharpe broth.

AIMS: To identify novel proteins secreted by the probiotic bacterium Lactobacillus rhamnosus GG after growth in de Mann-Rogosa-Sharpe broth (MRS), a complex medium often used for the culture of Lactobacillus. METHODS AND RESULTS: The proteins secreted by L. rhamnosus GG strain were precipitated using a trichloroacetic acid-based protocol, resolved by SDS-PAGE, and identified by tandem mass spectrometry (MS/MS). Among the proteins secreted by this bacterium, a leukocyte elastase inhibitor, already present in the MRS broth, was identified. Other proteins such as cell wall hydrolase, glyceraldehyde-3-phosphate dehydrogenase (GAPDH), phosphoglycerate kinase, and an extracellular transcriptional regulator have been also identified. CONCLUSIONS: Lactobacillus rhamnosus GG secretes several proteins during its growth in MRS, some of them with assigned functions in the prevention of the molecular mechanisms that lead to damage in the epithelial barrier (cell wall hydrolase) and in adhesion (GAPDH). The rest of the proteins require further genetic analysis in order to establish their precise roles. None of the proteins bound to mucin or fibronectin. SIGNIFICANCE AND IMPACT OF THE STUDY: Some of these secreted proteins could be involved in the probiotic effects exerted by L. rhamnosus GG strain, their identification being the first step towards in depth functional studies.

Identification of surface proteins involved in the adhesion of a probiotic Bacillus cereus strain to mucin and fibronectin.

Several Bacillus strains isolated from commercial probiotic preparations were identified at the species level, and their adhesion capabilities to three different model intestinal surfaces (mucin, Matrigel and Caco-2 cells) were assessed. In general, adhesion of spores was higher than that of vegetative cells to the three matrices, and overall strain Bacillus cereus(CH) displayed the best adhesion. Different biochemical treatments revealed that surface proteins of B. cereus(CH) were involved in the adhesion properties of the strain. Surface-associated proteins from vegetative cells and spores of B. cereus(CH) were extracted and identified, and some proteins such as S-layer components, flagellin and cell-bound proteases were found to bind to mucin or fibronectin. These facts suggest that those proteins might play important roles in the interaction of this probiotic Bacillus strain within the human gastrointestinal tract.

Lactobacillus plantarum 299v surface-bound GAPDH: a new insight into enzyme cell walls location.

The aim of this study was to provide new insight into the mechanism whereby the housekeeping enzyme glyceraldehyde-3-phosphate dehydrogenase (GAPDH) locates to cell walls of Lactobacillus plantarum 299v. After purification, cytosolic and cell wall GAPDH (cw-GAPDH) forms were characterized and shown to be identical homotetrameric active enzymes. GAPDH concentration on cell walls was growth-time dependent. Free GAPDH was not observed on the culture supernatant at any time during growth, and provoked cell lysis was not concomitant with any reassociation of GAPDH onto the cell surface. Hence, with the possibility of cw-GAPDH resulting from autolysis being unlikely, entrapment of intracellular GAPDH on the cell wall after a passive efflux through altered plasma membrane was investigated. Flow cytometry was used to assess L. plantarum 299v membrane permeabilization after labeling with propidium iodide (PI). By combining PI uptake and cw-GAPDH activity measurements, we demonstrate here that the increase in cw-GAPDH concentration from the early exponential phase to the late stationary phase is closely related to an increase in plasma membrane permeability during growth. Moreover, we observed that increases in both plasma membrane permeability and cw-GAPDH activity were delayed when glucose was added during L. plantarum 299v growth. Using a double labeling of L. plantarum 299v cells with anti-GAPDH antibodies and propidium iodide, we established unambiguously that cells with impaired membrane manifest five times more cw-GAPDH than unaltered cells. Our results show that plasma membrane permeability appears to be closely related to the efflux of GAPDH on the bacterial cell surface, offering new insight into the understanding of the cell wall location of this enzyme.

Serum IgG antibodies to P0 dimer and 35 kDa P0 related protein in neuropathy associated with monoclonal gammopathy.

BACKGROUND: Peripheral neuropathies (PN) associated with monoclonal gammopathy (MG) are widely considered as autoimmune disorders, but the putative role of incriminated antigens is still not understood. OBJECTIVE: Fifty five patients with PN associated with MG were studied to investigate whether new antigens could be found, and to evaluate their relation to clinical manifestations. METHODS: An immunological study was conducted on patient sera to identify autoreactivities against nerve proteins by western blotting. Antigen proteins were purified and analysed by proteomic tools. Correlation with ultrastrucural and clinical features was then studied. RESULTS: Of the 55 patients suffering from PN associated with MG, 17 exhibited IgG autoantibodies directed against peripheral nerve proteins of 35, 58, and 60 kDa. N-terminal microsequencing and mass spectrometry analyses of the 35 kDa protein revealed perfect peptidic matching with 47% of the amino acid sequence of P0, whereas the 58 and 60 kDa proteins were identified as the reduced and non-reduced forms of a P0 dimer. Deglycosylation did not affect IgG binding to the 35 kDa P0 related protein, suggesting a peptidic epitope. In contrast, deglycosylation abolished IgG recognition of the P0 dimer protein, so that a carbohydrate moiety may be implicated in the epitope formation. This confirmed the existence of two different types of IgG, one recognising the 58 and 60 kDa proteins and one directed against the 35 kDa protein. CONCLUSIONS: This is the first report of antibody activity directed against the dimeric association of P0. Although P0 oligomerisation and adhesion properties play a crucial part in the myelin sheath compaction, the pathogenic significance of these autoantibodies needs further investigations to be elucidated.

Mpe1, a zinc knuckle protein, is an essential component of yeast cleavage and polyadenylation factor required for the cleavage and polyadenylation of mRNA.

In Saccharomyces cerevisiae, in vitro mRNA cleavage and polyadenylation require the poly(A) binding protein, Pab1p, and two multiprotein complexes: CFI (cleavage factor I) and CPF (cleavage and polyadenylation factor). We characterized a novel essential gene, MPE1 (YKL059c), which interacts genetically with the PCF11 gene encoding a subunit of CFI. Mpe1p is an evolutionarily conserved protein, a homolog of which is encoded by the human genome. The protein sequence contains a putative RNA-binding zinc knuckle motif. MPE1 is implicated in the choice of ACT1 mRNA polyadenylation site in vivo. Extracts from a conditional mutant, mpe1-1, or from a wild-type extract immunoneutralized for Mpe1p are defective in 3'-end processing. We used the tandem affinity purification (TAP) method on strains TAP-tagged for Mpe1p or Pfs2p to show that Mpe1p, like Pfs2p, is an integral subunit of CPF. Nevertheless a stable CPF, devoid of Mpe1p, was purified from the mpe1-1 mutant strain, showing that Mpe1p is not directly involved in the stability of this complex. Consistently, Mpe1p is also not necessary for the processive polyadenylation, nonspecific for the genuine pre-mRNA 3' end, displayed by the CPF alone. However, a reconstituted assay with purified CFI, CPF, and the recombinant Pab1p showed that Mpe1p is strictly required for the specific cleavage and polyadenylation of pre-mRNA. These results show that Mpe1p plays a crucial role in 3' end formation probably by promoting the specific link between the CFI/CPF complex and pre-mRNA.

Analysis of protein sequences and protein complexes by matrix-assisted laser desorption/ionization mass spectrometry.

In the context of proteome analysis, matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) can fulfil the two tasks of primary structure verification and protein identification. As an illustration of the first of these tasks, the sequence of Eschericha coli isoleucyl-tRNA synthetase, a protein with 15 reported sequence conflicts, has been established by means of MALDI mass mapping. The identification of mitochondrial proteins participating in a yeast supramolecular complex exhibiting NADH dehydrogenase activity highlights the performances of MALDI-MS for the second task. The spectral suppression phenomenon occurring for complex peptide mixtures analysed by MALDI is discussed, as well as the role of post-source decay analysis for confident protein identification.

Yeast mitochondrial dehydrogenases are associated in a supramolecular complex.

Separation of yeast mitochondrial complexes by colorless native polyacrylamide gel electrophoresis led to the identification of a supramolecular structure exhibiting NADH-dehydrogenase activity. Components of this complex were identified by N-terminal Edman degradation and matrix-assisted laser desorption ionization mass spectrometry. The complex was found to contain the five known intermembrane space-facing dehydrogenases, namely two external NADH-dehydrogenases Nde1p and Nde2p, glycerol-3-phosphate dehydrogenase Gut2p, D- and L-lactate-dehydrogenases Dld1p and Cyb2p, the matrix-facing NADH-dehydrogenase Ndi1p, two probable flavoproteins YOR356Wp and YPR004Cp, four tricarboxylic acids cycle enzymes (malate dehydrogenase Mdh1p, citrate synthase Cit1p, succinate dehydrogenase Sdh1p, and fumarate hydratase Fum1p), and the acetaldehyde dehydrogenase Ald4p. The association of these proteins is discussed in terms of NADH-channeling.

N-Terminal domain of HTLV-I integrase. Complexation and conformational studies of the zinc finger.

The HTLV-I integrase N-terminal domain [50-residue peptide (IN50)], and a 35-residue truncated peptide formed by residues 9-43 (IN35) have been synthesized by solid-phase peptide synthesis. Formation of the 50-residue zinc finger type structure through a HHCC motif has been proved by UV-visible absorption spectroscopy. Its stability was demonstrated by an original method using RP-HPLC. Similar experiments performed on the 35-residue peptide showed that the truncation does not prevent zinc complex formation but rather that it significantly influences its stability. As evidenced by CD spectroscopy, the 50-residue zinc finger is unordered in aqueous solution but adopts a partially helical conformation when trifluoroethanol is added. These results are in agreement with our secondary structure predictions and demonstrate that the HTLV-I integrase N-terminal domain is likely to be composed of an helical region (residues 28-42) and a beta-strand (residues 20-23), associated with a HHCC zinc-binding motif. Size-exclusion chromatography showed that the structured zinc finger dimerizes through the helical region.

Valyl-tRNA synthetase from Escherichia coli MALDI-MS identification of the binding sites for L-valine or for noncognate amino acids upon qualitative comparative labeling with reactive amino-acid analogs.

Bromomethyl ketone derivatives of L-valine (VBMK), L-isoleucine (IBMK), L-norleucine (NleBMK) and L-phenylalanine (FBMK) were synthesized. These reagents were used for qualitative comparative labeling of Escherichia coli valyl-tRNA synthetase (ValRS), an enzyme with Val/Ile editing activity, in order to identify the binding sites for L-valine or noncognate amino acids. Labeling of E. coli ValRS with the substrate analog valyl-bromomethyl ketone (VBMK) resulted in a complete loss of valine-dependent isotopic [32P]PPi-ATP exchange activity. L-Valine protected the enzyme against inactivation. Noncognate amino acids analogs isoleucyl-, norleucyl- and phenylalanyl-bromomethyl ketones (IBMK, NleBMK and FBMK) were also capable of abolishing the activity of ValRS, FBMK being less efficient in inactivating the synthetase. Matrix-assisted laser desorption-ionization mass spectrometry designated cysteines 424 and 829 as the target residues of the substrate analog VBMK on E. coli ValRS, whereas, altogether, IBMK, NleBMK and FBMK labeled His266, Cys275, His282, His433 and Cys829, of which Cys275, His282 and His433 were labeled in common by all three noncognate amino-acid-derived bromomethyl ketones. With the exception of Cys829, which was most likely unspecifically labeled, the amino-acid residues labeled by the reagents derived from noncognate amino acids were distributed between two fragments 259-291 and 419-434 in the primary structure of E. coli ValRS. In fragment 419-434, Cys424 was specifically labeled by the substrate analog VBMK, while His433 was labeled in common by all the used bromomethyl ketone derivatives of noncognate amino acids, suggesting that the synthetic site where aminoacyl adenylate formation takes place on E. coli ValRS is built up of two subsites. One subsite containing Cys424 might represent the catalytic locus of the active center where specific L-valine activation takes place. The second subsite containing His433 might represent the binding site for noncognate amino acids. The fact that Cys275 and His282, fragment 259-291, were labeled by IBMK, NleBMK and FBMK, but not by the substrate analog VBMK, suggests that these residues might be located at or near the editing site of E. coli ValRS. Comparison of fragment 259-291 with all the available ValRS amino-acid sequences revealed that His282 is strictly conserved, with the exception of its replacement by a glycine in a subgroup corresponding to the archaebacteria. Because a nucleophile is needed in the editing site to achieve hydrolysis of an undesired product at the level of the carbonyl group thereof, it is proposed that the conserved His282 of E. coli ValRS is involved in editing.

Purification of the c-erbB2/neu membrane-spanning segment: a hydrophobic challenge.

High quality purification of membrane-spanning peptides and proteins remains a challenging problem. In this work we describe a tailored chromatographic purification of a synthetic 35-residue peptide corresponding to the transmembrane region of the tyrosine kinase receptor c-erb2/neu. Composed to over 70% by the amino acids alanine, isoleucine, leucine, phenylalanine and valine, this peptide presents a very hydrophobic character. Product isolation from the complex peptide mixture, obtained after acid cleavage of the resin matrix used during the solid-phase synthesis, represents a difficult task. We propose a three step strategy based on gel permeation and reversed-phase high-performance liquid chromatography, using aprotic polar solvent mixtures. The challenge consisted in obtaining a sufficient amount of an extremely pure sample, in order to allow structural analysis by NMR spectroscopy. Keeping trace of the synthetic peptide throughout the different purification steps was assured by MALDI TOF mass spectrometry, and the final product purity was checked by coupled liquid chromatography-ESI TOF mass spectrometry.

The second stalk of the yeast ATP synthase complex: identification of subunits showing cross-links with known positions of subunit 4 (subunit b).

A component of the stator of the yeast ATP synthase (subunit 4 or b) showed many cross-linked products with the homobifunctional reagent dithiobis[succinimidyl propionate], which reacts with the amino group of lysine residues. The positions in subunit 4 that were involved in the cross-linkings were determined by using cysteine-generated mutants constructed by site-directed mutagenesis of ATP4. Cross-linking experiments with the heterobifunctional reagent p-azidophenacyl bromide, which has a spacer arm of 9 A, were performed with mitochondria and crude Triton X-100 extracts containing the solubilized enzyme. Substitution of lysine residues by cysteine residues in the hydrophilic C-terminal part of subunit 4 allowed cross-links with subunit h from C98 and with subunit d from C141, C143, and C151. OSCP was cross-linked from C174 and C209. A cross-linked product, 4+beta, was also obtained from C174. It is concluded that the C-terminus of subunit 4 is distant from the membrane surface and close to F(1) and OSCP. The N-terminal part of subunit 4 is close to subunit g, as demonstrated by the identification of a cross-linked product involving subunit g and the cysteine residues 7 or 14 of subunit 4.

Chemical synthesis of yeast mitochondrial ATP synthase membranous subunit 8.

Chemical synthesis of highly hydrophobic peptides and proteins remains a challenging problem. Strong interchain associations within the peptide-resin matrix have to be overcome. A synthetic strategy for solid phase peptide synthesis is proposed, mainly based on prolonged coupling time using aprotic polar solvent mixtures. A tailored chromatographic purification was required to obtain a sample sufficiently pure for structural analysis. In this work, the total chemical synthesis of the membrane-embedded yeast mitochondrial ATP synthase subunit 8 is described. The quality of the synthetic protein was checked by electrospray mass spectrometry, its tendency to adopt alpha-helical secondary structure is evidenced by circular dichroism spectroscopy.

Purification, characterisation, and gene cloning of transglutaminase from Streptoverticillium cinnamoneum CBS 683.68.

The transglutaminase (TGase; EC 2.3.2.13) from Streptoverticillium cinnamoneum CBS 683.68 has been purified, characterised and its gene cloned. The purified enzyme had a relative molecular mass of 37,660 determined by mass spectrometry and contained a single Cys residue that was essential for the catalytic activity. Contrary to eukaryotic TGases, this enzyme was calcium-independent. The fact that TGase was capable to incorporate a wide variety of aliphatic and aromatic non-polar compounds suggested that the amine fixation site could be an hydrophobic pocket. S cinnamoneum CBS 683.68 TGase was synthesised as a protein precursor of 411 amino acid residues corresponding to a signal peptide of 81 amino acid residues and a mature TGase of 330 amino acid residues. Amino acid sequence analysis revealed that the S cinnamoneum CBS 683.68 TGase had little sequence homology with eukaryotic TGases, but shared high identity with the sequence of Streptoverticillium strain S-8112. In accordance with kinetics data, hydropathy analysis showed that the active site of the enzyme was in an hydrophobic environment as for eukaryotic TGases.

Combination of capillary electrophoresis and matrix-assisted laser desorption ionization mass spectrometry for glycosylation analysis of a human monoclonal anti-Rhesus(D) antibody.

Characterization of a human anti-Rhesus(D) monoclonal antibody, developed for the treatment of Rh(D) haemolytic disease of the newborn, was performed. Capillary electrophoresis (CE) has been employed for peptide mapping of the IgG heavy chain and glycopeptide identification. The combination of the high resolution and low solvent consumption of CE and the ultrasensitive detection and precise identification properties of mass spectrometry led to a complete glycosylation analysis of the protein. Glycopeptides were easily isolated from a single injection in a 100 microns i.d. capillary of the preparative CE system and collected for molecular mass determination using matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS). The off-line CE-MS characterization revealed the presence of different oligosaccharides linked to the unique N297-S-T glycosylation site of the IgG heavy chain. The differences between calculated and experimental masses of the glycopeptides suggested the presence of a fucosylated biantennary structure containing one or two galactose units as major oligosaccharide, together with similar species bearing a bisecting N-acetylglucosamine. CE conditions were optimized to allow the MS identification of sialylated forms.

Characterization of the chicken telokin heterogeneity by time-of-flight mass spectrometry.

Chicken gizzard telokin was purified to apparent homogeneity by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. This preparation yielded upon mass spectrometry analysis seven mass peaks spanning from 15 858 to 17 100 Da. Anion exchange-high performance liquid chromatography of the purified telokin revealed a high diversity of telokin molecules. By combining protein chemistry to chromatography and mass spectrometry, the telokin heterogeneity was analyzed. Three acetylated N-termini were found, AMI, MIS, and SGR. Cyanogen bromide cleavage of telokin yielded six different C-terminal peptides corresponding to the removal of one to six C-terminal glutamyl residues from the protein sequence deduced from the cDNA. Phosphorylation of telokin was detected, thus increasing the heterogeneity of the telokin preparation. In addition, peptide sequencing has shown that telokin contained either an aspartyl or a glutamyl residue at position 27, probably resulting from chicken polymorphism.

Posttranslational modifications of axonemal tubulin.

Axonemal tubulin exhibits a high degree of heterogeneity mostly due to several posttranslational modifications (PTM). The aim of this work was to chemically characterize the different PTM occurring in the C-terminal tail of axonemal tubulin purified from sea urchin, Paracentrotus lividus, spermatozoa. After its purification, tubulin was enzymatically cleaved. The C-terminal peptides were chromatographically isolated, first by anion exchange and then by reverse-phase HPLC. Peptides were characterized by their sequence, determined by Edman degradation, and by their mass, determined by MALDI-TOF/MS. The two major conclusions are that the majority of the isolated C-terminal peptides were unmodified and that polyglycylation and polyglutamylation can occur simultaneously on one molecule of alpha-tubulin.

Covalent methionylation of Escherichia coli methionyl-tRNA synthethase: identification of the labeled amino acid residues by matrix-assisted laser desorption-ionization mass spectrometry.

Methionyl-adenylate, the mixed carboxylic-phosphoric acid anhydride synthesized by methionyl-tRNA synthetase (MetRS) is capable of reacting with this synthetase or other proteins, by forming an isopeptide bond with the epsilon-NH2 group of lysyl residues. It is proposed that the mechanism for the in vitro methionylation of MetRS might be accounted for by the in situ covalent reaction of methionyl-adenylate with lysine side chains surrounding the active center of the enzyme, as well as by exchange of the label between donor and acceptor proteins. Following the incorporation of 7.0 +/- 0.5 mol of methionine per mol of a monomeric truncated methionyl-tRNA synthetase species, the enzymic activities of [32P]PPi-ATP isotopic exchange and tRNA(Met) aminoacylation were lowered by 75% and more than 90%, respectively. The addition of tRNA(Met) protected the enzyme against inactivation and methionine incorporation. Matrix-assisted laser desorption-ionization mass spectrometry designated lysines-114, -132, -142 (or -147), -270, -282, -335, -362, -402, -439, -465, and -547 of truncated methionyl-tRNA synthetase as the target residues for covalent binding of methionine. These lysyl residues are distributed at the surface of the enzyme between three regions [114-150], [270-362], and [402-465], all of which were previously shown to be involved in catalysis or to be located in the binding sites of the three substrates, methionine, ATP, and tRNA.

Structural and functional roles of a conserved proline residue in the alpha2 helix of Escherichia coli thioredoxin.

Proline 40 in Escherichia coli thioredoxin is located close to the redox active site (Cys32-Cys35) within the alpha2 helix. The conservation of this residue among most of the thioredoxins suggests that it could play an important role in the structure and/or function of this protein. We have substituted Pro40 for Ala by using site-directed mutagenesis and expressed the mutant P40A in E.coli. The effects of the mutation on the biophysical and biological properties of thioredoxin have been analyzed and compared with molecular dynamics simulations. Modeling predicted that the replacement of Pro40 by Ala induced a displacement of the active site which exposes Trp31 to the solvent and opens a cleft located between helices alpha2 and alpha3. The solvation free energy (SFE) calculation also indicated that P40A became more hydrophobic as W31 became more accessible. These predictions were totally in agreement with the experimental results. The mutant P40A exhibited chromatographic behavior and fluorescence properties very different from those of the wild-type (WT) protein, in relationship with the displacement of W31. The determination of the free energy of unfolding of P40A showed that the mutant was globally destabilized by 2.9 kcal/mol. However, the effect of the mutation on the transition curve was highly unusual as the midpoint of the unfolding transition increased, indicating that some local structures were actually stabilized by the mutation. Despite these structural modifications, neither the ability of the protein to reduce a chloroplastic enzyme nor its reactivity with the bacterial reductase decreased. The only functional difference was the higher stability of P40A in light activation of NADP-malate dehydrogenase under air, which suggests that the mutant was less rapidly re-oxidized than WT. Therefore, it can be concluded that Pro40 is not essential for maintaining the redox function of thioredoxin but rather is required for the stability of the protein.

Affinity labeling of Escherichia coli histidyl-tRNA synthetase with reactive ATP analogues. Identification of labeled amino acid residues by matrix assisted laser desorption-ionization mass spectrometry.

Recent affinity labeling studies have revealed that dimeric histidyl-tRNA synthetase from Escherichia coli displayed half-of-the-sites reactivity toward labeling with pyridoxal 5'-phosphate [Kalogerakos, T., Hountondji, C., Berne, P. F., Dutka, S. & Blanquet, S. (1994) Biochimie (Paris) 76, 33-44]. In the present report, affinity labeling studies were conducted by using other ATP analogues such as pyridoxal 5'-diphospho-5'-adenosine (pyridoxal-ppAdo), pyridoxal 5'-triphospho-5'-adenosine (pyridoxal-pppAdo), pyridoxal 5'-diphosphate (pyridoxal-P2) and 5'-p-fluorosulfonylbenzoyladenosine (FSO2BzAdo). The histidine-dependent isotopic [32P]PP/ATP exchange activity of His-tRNA synthetase was rapidly and completely lost upon incubation with either pyridoxal-ppAdo, pyridoxal-pppAdo or pyridoxal-P2, followed by reduction with sodium borohydride. Complete inactivation of His-tRNA synthetase corresponded to the incorporation of 2.8 mol of either pyridoxal-ppAdo or pyridoxal-P2/mol dimeric synthetase. Incubation of His-tRNA synthetase with FSO2BzAdo also resulted in a complete inactivation of the synthetase. However, contrasting with the pyridoxal derivatives, the plot of the residual enzymatic activity against the amount of covalently bound FSO2BzAdo appeared biphasic. In the early stages of inactivation, the relationship between the amount of residual activity and FSO2BzAdo incorporation was linear and extrapolated to a stoichiometry of 1.1 mol reagent/mol His-tRNA synthetase, suggesting that the labeling of one subunit was sufficient to inactivate one dimeric His-tRNA synthetase molecule. At longer incubation periods, additional reagent incorporation occurred and culminated at 2.5 mol label/mol His-tRNA synthetase. Excess of MgATP protected the enzyme against inactivation by either studied reagent. The labeled amino acid residues were identified by matrix-assisted-laser-desorption-ionization mass spectrometry, by measuring the peptide mass increase caused by the reagents. An identical set of four lysyl residues (Lys2, Lys118, Lys369 and Lys370 of His-tRNA synthetase) was found attached to pyridoxal-ppAdo or pyridoxal-P2. In addition, pyridoxal-ppAdo labeled the alpha-amino group of the N-terminal alanine. In a His-tRNA synthetase sample having incorporated 2.5 mol FSO2BzAdo/mol), the labeled amino acid residues were Lys118, Lys196, Tyr262 (or Tyr263), Lys369 and Lys377. Whatever the used reagent, Lys118 appeared to be the predominantly labeled residue, Lys118 belongs to fragment 112-124 (RHERPQK-GRYRQF) corresponding to motif 2 of class 2 aminoacyl-tRNA synthetases. The other modified lysyl residues (lysines 369, 370 and 377) are close to the catalytic motif 3, in the C-terminal region of the synthetase. Tyr262 and Tyr263 belong to a fragment 256-263 (LVRGLDYY) highly conserved among all known His-tRNA synthetase primary structures. Examination of the recently solved structure of crystalline E. coli His-tRNA synthetase [Amez, J. G., Harris, D. C., Mitschler, A., Rees, B., Francklyn, C. S. & Moras, D. (1995) EMBO J. 14, 4143-4155] shows that, with the exception of lysines 369, 370 and 377, the location of which may account for peculiar accessibility and reactivity, all the amino acid residues identified in this study map near the enzyme nucleotide-binding site, at the N-terminal catalytic domain of the synthetase.