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Multiple covalent modifications of Trg, a sensory transducer of Escherichia coli.

The sensory transducers of Escherichia coli are integral membrane proteins that mediate the tactic response of cells to chemical stimuli. Adaptation to environmental stimuli is correlated with methylation of the transducer proteins. Two transducer genes, tsr and tar, exhibit extensive homologies while no homology has been detected between a third transducer, trg, and those genes. The Tsr and Tar proteins have been shown to contain multiple sites for methylation as well as two sites for another modification that requires an active cheB gene product and is designated the CheB-dependent modification. In this study, covalent modifications of the Trg protein were characterized by analysis of tryptic peptides. We found that methylation occurred at several sites on the Trg protein and that the protein contained at least three sites for CheB-dependent modification, two of which were located on a tryptic peptide that contains both methionine and lysine. This tryptic peptide is analogous to the methionine- and lysine-containing methyl-accepting peptides isolated from the Tsr and Tar proteins and like those peptides may contain several methyl-accepting sites. We estimated the pKa of the group created by the CheB-dependent modification on the methionine- and lysine-containing peptide of Trg to be between pH 2.2 and 5.8. This result supports the idea that the CheB-dependent modification is an enzymatic deamidation of glutamine to glutamic acid.

Bacterial Proteins↗

Arginine modification in elastase. Effect on catalytic activity and conformation of the calcium-binding site.

Chemical modification of 2 +/- 0.5 arginine residues of porcine pancreatic elastase by 1,2-cyclohexanedione leads to an 85 +/- 5% loss of activity with the specific substrate N-succinyltrialanine p-nitroanilide. Modification of additional arginines does not completely abolish the enzyme activity. The modification reaction is very fast (second order rate constant = 0.24 M-1 S-1) and involves only arginine residues. Acetyltetraalanine or trifluoroacetyltetraalanine decreases the rate of cyclohexanedione-induced inactivation of the enzyme but does not significantly change the number of modified arginine residues. Other dicarbonyl reagents, butanedione or phenylglyoxal, also react with elastase but at much lower rates. Cyclohexanedione-modified elastase is partially active against a series of synthetic substrates of varying chain length. The partial inhibition results from a 2- to 5-fold increase in Km while kappa cat is increased for most substrates. For N-succinyltrialanine p-nitroanilide both the acylation and deacylation rate constants are decreased. The Ki values of a series of acetylated and trifluoroacetylated inhibitors increase 2- to 5-fold. Modified elastase is still able to react with fibrous elastin and with plasma alpha 1-proteinase inhibitor but at significantly lower rates. Modification of one arginine residue alters the properties of the calcium-binding site of elastase as demonstrated by terbium luminescence experiments. The affinity of enzyme for terbium is decreased by a factor of 10 and the circularly polarized luminescence spectrum of the terbium-elastase complex is considerably flattened. Modification of further arginine residues does not increase the extent of these alterations. Circular dichroism shows that the overall conformation of elastase is not altered following arginine modification. We speculate that the two residues modified by cyclohexanedione are Arg 65, located at about 8 A from the metal ion-binding site, and Arg 217A, located at the S'3 subsite of elastase.

Animals↗

Behavioral modification in a weight-reduction program.

Previous surveys have shown a high prevalence of obesity in women of low socioeconomic status. This study confirmed the relationship in the Medical Appointment Clinic at Grady Memorial Hospital, Atlanta. Behavioral modification therapy for obesity had not been carefully tested in this type of population. Therefore, a behavioral modification group-oriented weight-reduction method was adapted for 80 participants from this setting. Eighty controls, matched for age, sex, race, and percent ideal body weight, received individualized counseling from a dietitian. Thirty-one matched pairs (62 individuals) had follow-up weights taken more than one year later. Thirteen percent (four) of the behavioral modification group participants versus 6.4% (two) of the control participants maintained a loss of 20 lb. or more during this period. The mean weight loss for the behavioral modification group was 4.6% of their ideal body weight versus 0.9% for the control group. The results of the behavioral modification program were statistically superior to those of the control program (p = 0.058). Overall, for participants whose mean weight was 241 lb., it is difficult to conclude that a mean 5-lb. weight loss represents a meaningful change or that this weight loss was due to behavioral modification. The results of this program among low socioeconomic status women, however, were comparable with the results of similar large, free-living programs among middle class participants.

Adult↗

[Serological characterization of bacteriophage T3 carrying different "non-classical" modifications].

The antigenic properties of bacteriophage T3 and a mutant T3/R7 which undergoes "non-classical" modification and restriction are compared. The "non-classical" modification of T3/R7 consists of a host-dependent, reversible change in the adsorption capacity of phage on different host strains. We have shown that this modification is connected with changes in the antigenic properties of phage components involved in phage absorption to the host cell. This means that, in contrast to the "classical" host-control-led modification and restriction of DNA, the "non-classical" modification and restriction of phage is based on protein modification.

Adsorption↗

Methods of utilization of regularities in modificational variability of quantitative characters in plant breeding.

The nature of the modificational and genotypic variability of 30 quantitative characters in wheat varieties with different numbers of genes for dwarfing, and nine characters in contrasting pea varieties, differing in leaf type, was investigated. The experimental data, obtained in 1971--1974 and analyzed in the M-220M and Minsk-22 computers, showed a high degree of similarity in the modificational variability of similar quantitative characters for all varieties of the same crop. Significant similarities were also found in the modificational variability of identical quantitative characters for the two species (wheat and peas), which showed that the regularities in modificational variability are generally applicable in biology. The coefficients of variation, calculated from the total data obtained, for modificational (CVm), genotypic (CVg) and overall modificational-genotypic (CVm+g) variability, for the different quantitative characters, may be useful criteria in plant breeding. They may reveal genotypic differences in the quantitative characters in hybrids and mutant populations, and may thus be useful in improving the efficiency of selection of wheat and pea strains.

Agriculture↗

Evaluation of a modification of the Hudson demand valve in ventilated and spontaneously breathing horses.

Hypoxaemia commonly develops during general anaesthesia and in the recovery period in horses. The Hudson demand valve has been used to increase arterial PO2, but it has been found to increase airway resistance considerably when used during spontaneous ventilation. This paper evaluates a modification of the valve designed to reduce this resistance. The effects of the valve and its modification on arterial oxygen (PaO2), and carbon dioxide (PaCO2) tensions were evaluated in four ponies anaesthetised by a total intravenous technique. The valve increased PaO2 from 8.3 +/- 1.1 to 32.7 +/- 7.6 kPa during spontaneous ventilation and to 44.2 +/- 7.4 kPa during intermittent positive pressure ventilation. With the modification, the PaCO2 was increased to 9.0 +/- 2.5 kPa during spontaneous ventilation PaO2 was unchanged by the valve (7.2 +/- 0.4 kPa to 7.1 +/- 0.7 kPa) but it was reduced to 6.4 +/- 0.9 kPa with the modification. The valve was also evaluated in 20 clinical cases during their recovery from halothane anaesthesia. It increased PaO2 from 7.4 +/- 2.1 kPa to 17 +/- 18.3 kPa during spontaneous ventilation and from 8.0 +/- 1.8 kPa to 23.4 +/- 22.2 kPa during positive pressure ventilation. With the modification, PaO2 was increased from 7.8 +/- 1.4 kPa to 10.4 +/- 3.8 kPa during spontaneous ventilation and from 7.6 +/- 1.5 kPa to 14.8 +/- 8.4 kPa during positive pressure ventilation. During spontaneous ventilation PaCO2 was increased from 5.9 +/- 0.4 kPa to 6.2 +/- 0.6 kPa with the unmodified valve and from 6.3 +/- 0.5 kPa to 6.6 +/- 0.5 kPa with the modification.(ABSTRACT TRUNCATED AT 250 WORDS)

Anesthesia, General↗

Post-translational modifications of water-soluble human lens crystallins from young adults.

Post-translational modifications of the water-soluble human lens crystallins from young adult donors were identified and located using electrospray ionization mass spectrometric analysis of the intact proteins and fast atom bombardment mass spectrometry of enzymatic digests. Peptides corresponding to all of the sequences of alpha A-, alpha B-, and beta B2-crystallins were found, permitting the entire sequences to be searched for modifications. The major portions of these three crystallins were not modified. Modifications of alpha A-crystallin that were detected included 2 phosphorylated Ser residues (1 of which appears to be unique to human lenses), deamidation at some Gln and Asn residues, a disulfide bond between Cys-131 and Cys-142, and loss of the COOH-terminal Ser residue. Three phosphorylated Ser residues, but no deamidation, were found in alpha B-crystallin. The molecular weights of neither the intact protein nor the peptides in the enzymatic digests indicated any post-translational modification of the principal beta-crystallin, beta B2. The molecular weights of the other beta- and gamma-crystallins for which sequences have been published suggested the presence of post-translational modifications or errors in the published sequences. Although enough peptides were found to establish the presence of specific proteins, peptides corresponding to all portions of these proteins were not found, and elucidation of these structures is not yet complete. This mass spectrometric characterization of the total water-soluble proteins from normal young adult lenses provides a reference data base for future investigations of the modifications present in aged and cataractous lenses.

Adult↗

Identification of the physical modification threshold of dentin induced by neodymium and holmium YAG lasers using scanning electron microscopy.

Laser application to dentin has been advocated to modify the dentin substrate for restorative procedures. We examined the minimum energy density required to physically modify the dentin surface using 1.06 microns and 1.32 microns Neodymium:Yttrium-Aluminum-Garnet (Nd:YAG) and 2.10 microns Holmium-YAG (Ho:YAG) lasers. Three millimeter thick dentin sections from the middle occlusal third of crowns of third molars were used. To determine the effect of surface preparation, the sections were ground to 240, 320, 400, 600 grit or polished to 0.5 micron. Smear layer was removed using 0.5 M EDTA for 2 minutes. Five single pulse repetitions at each laser parameter were performed. Power (W) and energy per pulse (mJ/p) were increased for each wavelength until a physical modification occurred. The energy density (J/cm2) was then held constant and the threshold was confirmed using 200, 320 and 550 microns diameter quartz contact probes. Scanning electron microscopy (SEM) was used to verify the physical modification of the dentin. The physical threshold remained constant for ground and polished surfaces. Similar surface modifications were found for the three wavelengths tested. The threshold modifications occurred at 207, 165, and 83 J/cm2 for the 1.06 microns, 1.32 microns and 2.10 microns lasers, respectively. For all emission wavelengths tested the physical threshold modification occurred at relatively low energy densities. These lasers show promise for surface modification of dentin.

Aluminum↗

[Modification of RNA ligase histidine residues by diethylpyrocarbonate].

The practicality of Tris-HCl buffer for modification of histidine residues by diethylpyrocarbonate (DEPC) was studied using a model protein-hexokinase. It was found that modification was selective at pH 7.5. Conditions for modification of one histidine residue in the protein molecule were specified. In 30 mM Tris-HCl buffer pH 7.5, 10-min interaction of RNA-ligase with 0.3 mM DEPC was accompanied by modification of one histidine residue, as a result of which the ability to form a covalent AMP-RNA-ligase complex decreased 3 times. Modification of two histidine residues of RNA-ligase resulted in a complete loss of the enzyme activity. At increasing DEPC concentration modification affected all of the seven histidine residues of RNA-ligase. The kinetic parameters (Km and V) for the native and modified enzymes were determined and compared.

Diethyl Pyrocarbonate↗

Enhanced modifications of low-density lipoproteins (LDL) by endothelial cells from smokers: a possible mechanism of smoking-related atherosclerosis.

OBJECTIVE: The aim of the study was to investigate LDL modifications by cultured human umbilical vein endothelial cells (HUVEC) from women smokers and non-smokers. METHODS: Modifications of LDL by HUVEC were studied by determining the values of thiobarbituric acid-reactive substances (TBARS) and the percentage of the most electronegative oxidized LDL fraction (fraction C) by using an ion-exchange chromatographic method based on fast protein liquid chromatography (FPLC). We also studied the cellular production of superoxide anion, the effect of various inhibitors and cysteine, and determined total intracellular glutathione content and cell growth. RESULTS: LDL exposed to HUVEC from smokers for 48 h showed significantly greater modifications than LDL exposed to HUVEC from non-smokers, as assessed by TBARS determination (19.4 +/- 1.2, mean +/- s.e.m., n = 20 versus 15.4 +/- 0.7 nmol/mg LDL, n = 19; P < 0.01) and by FPLC (percentage of fraction C: 39 +/- 7, n = 29 versus 14 +/- 3, n = 34; P < 0.001). Moreover, HUVEC from smokers produced significantly more superoxide anion than those from non-smokers (0.46 +/- 0.13 nmol/10(5) cell/min, n = 9 versus 0.22 +/- 0.05, n = 10; P < 0.05). Superoxide production, like cell-induced modification of LDL, was strongly dependent on the presence of cysteine in the medium. Furthermore, HUVEC from smokers had a significantly (P < 0.05) higher total intracellular glutathione content than those from non-smokers (39.9 +/- 3.1 nmol/mg, n = 9 versus 31.8 +/- 2.2, n = 7). Finally, HUVEC from smokers and non-smokers showed similar growth at 48 h. CONCLUSION: HUVEC from smokers converted significantly more LDL into an atherogenic form than HUVEC from non-smokers, a phenomenon that was not due to altered cell growth. HUVEC-mediated LDL modifications were strongly thiol-dependent, as both LDL modifications and superoxide anion production were inhibited in cysteine-free medium. Stimulation of cystine uptake by HUVEC, reflected by the enhanced total glutathione content, could account for the enhanced superoxide anion production. All these observations may be relevant to the pathophysiology of smoking-related cardiovascular disease.

Adult↗

Effect of homocysteine on copper ion-catalyzed, azo compound-initiated, and mononuclear cell-mediated oxidative modification of low density lipoprotein.

Homocysteine is an independent risk factor for cardiovascular diseases. The mechanisms by which elevated plasma concentrations of homocysteine are related to the pathogenesis of atherosclerosis are not fully understood. To examine whether homocysteine is implicated in atherogenesis through the modification of low density lipoprotein (LDL), the effect of homocysteine on the oxidation of LDL was studied by three different oxidation systems. Thus, LDL was subjected to Cu(2+)-catalyzed, azo compound-initiated, and peripheral blood mononuclear cell-mediated oxidative modification. The extent of modification was assessed by measuring the formation of conjugated dienes, lipid peroxides, thiobarbituric acid-reactive substances, and the relative electrophoretic mobility. Homocysteine at a normal plasma concentration (6 microM) showed no effect, whereas a concentration corresponding to moderate hyperhomocysteinemia (25 microM) or to concentrations seen in homocystinuria patients (100, 250, and 500 microM) protected LDL from modification of the lipid as well as of the protein moiety. One exception was observed: when the oxidation was initiated by copper ions, homocysteine at concentrations 6 and 25 microM stimulated the lipid peroxidation of LDL to a small, but statistically significant extent. High concentrations of homocysteine showed antioxidative properties as long as the thiol groups were intact, thereby delaying the onset of the oxidation. The 1,1-diphenyl-2-picrylhydracyl radical test demonstrated that homocysteine at concentrations > or = 50 microM possessed marked free radical scavenging capacity. Finally, LDL isolated from two patients with homozygous homocystinuria showed similar extent of Cu(2+)-catalyzed oxidation as LDL from a group of healthy control subjects. Taken together, our data suggest that low concentrations of homocysteine in the presence of copper ions may enhance the lipid peroxidation of LDL, whereas high concentrations of homocysteine may protect LDL against oxidative modification in the lipid as well as in the protein moiety. Thus, homocysteine-induced atherosclerosis may be explained by mechanisms other than oxidative modification of low density lipoprotein.

Adolescent↗

Chemical modifications and dissociation characteristics of tyrosine and tryptophan residues in alpha-crystallin.

A quantitative estimation of surface accessibility of aromatic residues in alpha-crystallin from goat lens has been accomplished by chemical modifications using different specific reagents having varying sizes. Results of modification of tyrosine residues with N-acetylimidazole and tetranitromethane when combined with those of ionization studies carried out with hydroxyl ions having the smallest size reveal different classes of tyrosine residues in the native protein: 78 +/- 2 residues have been found to be easily available for modification; among the rest, 94 +/- 2 residues appear to be comparatively less exposed to the reagents while 28 +/- 2 residues are found to be completely unavailable for modification in the native protein and are modified only when the protein is denatured. Modification of tryptophan residues with H2O2 also indicates different classes of these residues available for oxidation at different concentrations of the oxidant. 34 +/- 2 residues of tryptophan are found to be easily oxidized at a lower concentration of H2O2 during the first phase of the reaction. The remaining tryptophan residues appear to be less exposed to the reagent. This is also corroborated from the studies of reactivities of these residues towards another specific but bulkier reagent, 2-hydroxy-5-nitrobenzyl bromide. These surface exposed aromatic residues in alpha-crystallin may be considered to be vulnerable to in vivo oxidative modifications forming insoluble aggregates which may finally contribute to the formation of cataract.

Crystallins↗

Increased protein flexibility leads to promiscuous protein--DNA interactions in type IC restriction-modification systems.

We have investigated the role of a four amino acid element that is repeated twice and three times, respectively, in the specificity polypeptides of the two allelic restriction-modification systems EcoR124 and EcoR124/3. We had earlier shown that this difference in amino acid sequence between the two systems is solely responsible for the different DNA sequence specificities of the two systems. The effect of single amino acid substitutions and small insertion and deletion mutations on restriction activity and modification specificity was determined in vivo by phage infection assays and in vitro by methylation of DNA with purified modification methylases. Mutant restriction-modification systems with changes in the number and the length of the central amino acid repeats exhibited decreased restriction activity and in some cases relaxed substrate specificity. Our data strongly support the idea that the repetitive amino acid motif in the specificity polypeptides forms part of a flexible interdomain linker. It may be responsible for positioning on the DNA the two major specificity polypeptide domains which are thought to contact independently the half sites of the split recognition sequences typical for all type I restriction-modification systems.

Alleles↗

MapID-based quantitative mapping of chemical modifications and expression of human transfer RNA.

Detection and quantification of tRNA chemical modifications are critical for understanding their regulatory functions in biology and diseases. However, tRNA-seq-based methods for modification mapping encountered challenges both experimentally (poor processivity of heavily modified tRNAs during reverse transcription or RT) and bioinformatically (frequent reads misalignment to highly similar tRNA genes). Here, we report "MapID-tRNA-seq" where we deployed an evolved reverse transcriptase (RT-1306) into tRNA-seq and developed "MapIDs" that reduce redundancy of the human tRNA genome and explicitly annotate genetic variances. RT-1306 generated robust mutations against m1A and m3C, and RT stops against multiple bulky roadblock modifications. MapID-assisted data processing enabled systematic exclusion of false-positive discoveries of modifications which arise from reads misalignment onto similar genes. We applied MapID-tRNA-seq into mapping m1A, m3C and expression levels of tRNAs in three mammary cell lines, which revealed cell-type dependent modification sites and potential translational regulation of the reduced mitochondrial activities in breast cancer.

Humans↗

Analytical challenges for mapping non-canonical and non-protein ubiquitin/Ubl modifications by mass spectrometry.

INTRODUCTION: Covalent modification by ubiquitin via Lys isopeptide bonds is fundamental for regulating protein turnover and function. Additionally, ubiquitin esterification occurs on Ser/Thr/Tyr residues in proteins and on non-proteinaceous substrates including ribose, saccharides, lipids, and small molecule drugs. Ubiquitin posttranslational modifications may therefore be much more widespread across cell biological pathways. Recent literature (PubMed) reflects the increased interest in analytical methods for mapping of non-canonical substrates modified by ubiquitin and ubiquitin-like (UBL) proteins. AREAS COVERED: Mass spectrometry (MS)-based methodologies involve advanced proteomic techniques to identify ubiquitin modifications on amino acids other than Lys, such as Ser, Thr, Tyr and Cys as well as protein N-termini. After digestion, standard MS workflows identify canonical ubiquitination by detecting a ubiquitin C-terminal tag attached to the amine side chains of Lys residues of substrate-derived peptides suitable for MS/MS sequencing. For non-canonical modifications on proteins and substrates other than proteins, specialized strategies are required, such as using antibodies to enrich N-terminally modified peptides in combination with using high-resolution MS/MS based on softer fragmentation technologies to detect esterification and possibly other types of substrate modifications. EXPERT OPINION: Enabling such technologies will reveal a previously unrecognized angle of the ubiquitin code's complexity in cells.

Humans↗

A DNA methyltransferase can protect the genome from postdisturbance attack by a restriction-modification gene complex.

In prokaryotic genomes, some DNA methyltransferases form a restriction-modification gene complex, but some others are present by themselves. Dcm gene product, one of these orphan methyltransferases found in Escherichia coli and related bacteria, methylates DNA to generate 5'-C(m)CWGG just as some of its eukaryotic homologues do. Vsr mismatch repair function of an adjacent gene prevents C-to-T mutagenesis enhanced by this methylation but promotes other types of mutation and likely has affected genome evolution. The reason for the existence of the dcm-vsr gene pair has been unclear. Earlier we found that several restriction-modification gene complexes behave selfishly in that their loss from a cell leads to cell killing through restriction attack on the genome. There is also increasing evidence for their potential mobility. EcoRII restriction-modification gene complex recognizes the same sequence as Dcm, and its methyltransferase is phylogenetically related to Dcm. In the present work, we found that stabilization of maintenance of a plasmid by linkage of EcoRII gene complex, likely through postsegregational cell killing, is diminished by dcm function. Disturbance of EcoRII restriction-modification gene complex led to extensive chromosome degradation and severe loss of cell viability. This cell killing was partially suppressed by chromosomal dcm and completely abolished by dcm expressed from a plasmid. Dcm, therefore, can play the role of a "molecular vaccine" by defending the genome against parasitism by a restriction-modification gene complex.

Animals↗

Mobility of a restriction-modification system revealed by its genetic contexts in three hosts.

The flow of genes among prokaryotes plays a fundamental role in shaping bacterial evolution, and restriction-modification systems can modulate this flow. However, relatively little is known about the distribution and movement of restriction-modification systems themselves. We have isolated and characterized the genes for restriction-modification systems from two species of Salmonella, S. enterica serovar Paratyphi A and S. enterica serovar Bareilly. Both systems are closely related to the PvuII restriction-modification system and share its target specificity. In the case of S. enterica serovar Paratyphi A, the restriction endonuclease is inactive, apparently due to a mutation in the subunit interface region. Unlike the chromosomally located Salmonella systems, the PvuII system is plasmid borne. We have completed the sequence characterization of the PvuII plasmid pPvu1, originally from Proteus vulgaris, making this the first completely sequenced plasmid from the genus Proteus. Despite the pronounced similarity of the three restriction-modification systems, the flanking sequences in Proteus and Salmonella are completely different. The SptAI and SbaI genes lie between an equivalent pair of bacteriophage P4-related open reading frames, one of which is a putative integrase gene, while the PvuII genes are adjacent to a mob operon and a XerCD recombination (cer) site.

Amino Acid Sequence↗

Normal and transforming Ras are differently regulated for posttranslational modifications.

Point mutation of the c-H-ras gene significantly increases cellular transforming activities of Ras. Since posttranslational modification and subsequent membrane localization are essential for the biological activities of Ras, we examined whether or not the mutation also affects these two factors. The normal (Gly(12)) or the transforming (Val(12)) c-H-ras gene was expressed in NIH3T3 cells using a metallothionein promoter. Expression of either type of Ras was efficiently induced by the cadmium treatment of these cells, and immunoprecipitation of metabolically labeled cell extracts revealed that both normal and transforming Ras were expressed as four differently migrating forms on SDS-polyacrylamide gels, two of which were slower migrating cytosolic precursors and the other two were faster migrating membrane-bound forms. There was no significant difference in half lives between normal and transforming Ras; however, posttranslational modification was quite different between the two types of Ras. Transforming Ras was processed and became membrane-bound forms much more efficiently than normal Ras. Interestingly, posttranslational modification and membrane localization of Ras was significantly inhibited when the c-myc oncogene was co-expressed with Ras. In contrast to the c-myc oncogene, expression of either wild type or mutant p53 did not affect the posttranslational modification of Ras, suggesting that the c-myc oncogene specifically impairs the posttranslational modification of Ras.

3T3 Cells↗