Cross-talk between Diverse Serine Integrases

Phage-encoded serine integrases are large serine recombinases that mediate integrative and excisive site-specific recombination of temperate phage genomes. They are well suited for use in heterologous systems and for synthetic genetic circuits as the attP and attB attachment sites are small (< 50 bp), there are no host factor or DNA supercoiling requirements, and they are strongly directional, doing only excisive recombination in the presence of a recombination directionality factor. Combining different recombinases that function independently and without cross-talk to construct complex synthetic circuits is desirable, and several different serine integrases are available. However, we show here that these functions are not reliably predictable, and we describe a pair of serine integrases encoded by mycobacteriophages Bxz2 and Peaches with unusual and unpredictable specificities. The integrases share only 59% amino acid sequence identity and the attP sites have fewer than 50% shared bases, but they use the same attB site and there is non-reciprocal cross-talk between the two systems. The DNA binding specificities do not result from differences in specific DNA contacts but from the constraints imposed by the configuration of the component half-sites within each of the attachment site DNAs.     

Further studies on the peptido-galactomannan from the yeast form of Cladosporium werneckii. Identification of O-acetyl substituents and isolation of the peptide components following beta-elimination.

The pathogenic yeast Cladosporium werneckii produces a surface peptido-phosphogalactomannan (PPGM) with a peptide backbone rich in serine and threonine to which three types of carbohydrate chains are linked. These chains are: Type a, glactomannan units linked through phosphodiester bonds to produce long chains of molecular weight about 50,000; type b more numerous short mannosyl oligosaccharide units, and type c, more infrequent, long galactomannan chains. The first two are linked to the peptide through alkali-labile bonds to serine and threonine of the peptide whereas type c chains are linked through alkali-stable bonds (Lloyd, K. O. (1972) Biochemistry, 11, 3884–3890). The PPGM sample can be separated into three or four major components by diethylaminoethyl (DEAE-) Sephadex chromatography. By means of sequential degradations with alkali and acid, the structural basis for this heterogeneity has been demonstrated. It is due to the presence of different proportions of the three types of chains in the various fractions. The presence of O-acetyl groups, mainly on the a chains, was demonstrated in PPGM by chemical analysis and by proton and ¹³C nuclear magnetic resonance spectroscopy. Purified a chains were isolated from PPGM following Pronase digestion. By taking advantage of the alkali lability of the carbohydrate-protein linkages it has been possible to cleave the peptide moiety away from the carbohydrate. By sequential chromatography on Bio-Gel P-100, Dowex 1 and Bio-Gel P-100, five modified peptide fractions were isolated. The molecular weights of these fractions varied from 9,500 to 18,500 as judged by polyacrylamide-gel electrophoresis. Unlike the original peptide, the modified peptides contained low amounts of serine and threonine. The predominant amino acids were alanine, glycine, aspartic acid and glutamic acid which together make up between 51 and 55% of the peptides. The high content of the last two amino acids accounts for the acidic nature of the peptides. It appears that each fraction consists of a slightly heterogeneous population of peptides very similar in amino acid composition. It is not clear whether the compositional and size heterogeneity exists in the original peptide or whether it arose during the isolation procedure.     

The role of energy,serine, glycine,and 1-carbon units in the cost of nitrogen excretion in mammals and birds

The efficiency with which dietary protein is used affects the nitrogen excretion by the animal and the environmental impact of animal production. Urea and uric acid are the main nitrogen excretion products resulting from amino acid catabolism in mammals and birds, respectively. Nitrogen excretion can be reduced by using low-protein diets supplemented with free amino acids to ensure that essential amino acids are not limiting performance. However, there are questions whether the capacity to synthesize certain nonessential amino acids is sufficient when low-protein diets are used. This includes glycine, which is used for uric acid synthesis. Nitrogen excretion not only implies a nitrogen and energy loss in the urine, but energy is also required to synthesize the excretion products. The objective of this study was to quantify the energy and metabolic requirements for nitrogen excretion products in the urine. The stoichiometry of reactions to synthesize urea, uric acid, allantoin, and creatinine was established using information from a publicly available database. The energy cost was at least 40.3, 60.7, 64.7, and 65.4 kJ/g excreted N for urea, uric acid, allantoin, and creatinine, respectively, of which 56, 56, 47, and 85% were retained in the excretion product. Data from a broiler study were used to carry out a flux balance analysis for nitrogen, serine, glycine, and so-called 1-carbon units. The flux balance indicated that the glycine intake was insufficient to cover the requirements for growth and uric acid excretion. The serine intake was also insufficient to cover the glycine deficiency, underlining the importance of the de novo synthesis of serine and glycine. One-carbon units are also a component of uric acid and can be synthesized from serine and glycine. There are indications that the de novo synthesis of 1-carbon units may be a “weak link” in metabolism, because of the stoichiometric dependency between the synthesized 1-carbon units and glycine. The capacity to catabolize excess 1-carbon units may be limited, especially in birds fed low-protein diets. Therefore, there may be an upper limit to the 1-carbon-to-glycine requirement ratio in relation to nutrients that supply 1-carbon units and glycine. The ratio can be reduced by increasing uric acid excretion (i.e., reducing protein deposition) or by dietary supplementation with glycine. The hypothesis that the 1-carbon-to-glycine requirement ratio should be lower than the supply ratio provides a plausible explanation for the growth reduction in low-protein diets and the positive response to the dietary glycine supply.     

Effects of the bumblebee (Bombus ignitus) venom serine protease inhibitor on serine protease and phospholipase A2 of B. ignitus venom

Bumblebee venom contains serine proteases and serine protease inhibitors. In this study, we characterized whether the bumblebee (Bombus ignitus) venom serine protease inhibitor (Bi-KTI) inhibits B. ignitus venom serine protease (Bi-VSP) or phospholipase A₂ (Bi-PLA₂). Bi-KTI did not inhibit Bi-VSP activity at pH 5.4 or 7.4, whereas Bi-KTI slightly inhibited Bi-VSP activity at pH 7.4 after a 30 min preincubation. The Bi-VSP activity that converts prothrombin into thrombin and fibrin into fibrin degradation products was not significantly affected by Bi-KTI. Additionally, Bi-KTI or Bi-VSP did not inhibit Bi-PLA₂ activity. These findings indicate that each bee venom component appears to a play a toxic role via a unique function.     

Spore germination and carbon metabolism inFusarium solani: VI. Ethanol metabolism and the biosynthesis of amino acids

Although macrospore germination inFusarium solani requires ethanol under specified cultural conditions, it is not likely that this has any general significance in nature; the requirement is strain-specific and can be modified by the growth medium on which spores are produced. Under the conditions in which ethanol is required it is fully replaced by serine, but it is partially and only at relatively high concentrations replaced by threonine, arginine, and glutamine. Inhibitor and incorporation experiments show that ethanol is converted to serine by a metabolic route that requires the action of ethanol dehydrogenase but does not involve glycine, acetate, or the tricar☐ylic acid cycle. Overall ethanol metabolism, however, does involve acetate or acetyl-coenzyme A, as evidenced by a partial inhibition of it by fluoroacetate. Spores metabolizing labeled acetate, which does not replace ethanol in spore germination, incorporate label into several amino acids but not into serine, while serine is the first and most prominent amino acid product of ethanol metabolism.     

Substitution of serine caused by a recessive lethal suppressor in yeast.

The SUP-RL1 suppressor in the yeast Saccharomyces cerevisiae causes lethality in haploid strains but not in diploid or aneuploid strains that are heterozygous for the suppressor locus. This recessive lethal suppressor acts on amber (UAG) nutritional markers, and can cause the production of approximately 50% of the normal amount of iso-1-cytochrome c in disomic strains that are heterozygous for the SUP-RL1 suppressor, and that contain the cyc1-179 allele which has an amber codon corresponding to amino acid position 9. The suppressed iso-1-cytochrome c contains a residue of serine at the position that corresponds to the site of the amber codon. SUP-RL1 was found to lie between thr4 and MAL2 on chromosome III, approximately 30 map units from the mating-type locus. It is suggested that the gene product of SUP-RL1 may be a species of serine transfer RNA that normally reads the serine codon UCG, and that is represented only once in the haploid genome.     

Purification and characterization of an alkaline protease from Oerskovia xanthineolytica TK-1

Alkaline protease from Oerskovia xanthineolytica TK-1 was purified to an electrophoretically homogeneous state by phenyl-Sepharose CL-4B and DEAE-Sephacel. The molecular mass of the enzyme was 20,000 Da by SDS-polyacrylamide gel electrophoresis. The enzyme was most active at pH 9.5–11.0 and 50°C. It was inhibited by inhibitors of serine protease. The enzyme preferentially hydrolyzed the ester of phenylalanine among N-CBZ amino acid p-nitrophenol esters. These results indicate that the protease can be classified as an alkaline serine protease.     

Methods for the identification of N-asparaginyl and O-seryl/threonyl glycosidic linkages to aminosugars in glycoproteins

Methods are presented for the identification of certain glycopeptide bonds in glycoproteins. Mucin-type linkages are determined following treatment of glycoproteins with alkaline sodium [³H]borohydride. Such treatment cleaves O-glycosidic bonds to serine and threonine and simultaneously labels the sugar and amino acid components of the linkage. Following acid hydrolysis and dansylation, the sugar component of the linkage is identified as its corresponding dansyl-hexosaminitol by fluorographic techniques. A method is described for the separation of dansyl-galactosaminitol and dansyl-glucosaminitol by thin-layer electrophoresis in borate buffers. The amino acid component of the glycopeptide linkage is identified by fluorography following two-dimensional thin-layer chromatography of its dansyl derivative on polyamide plates. For the analysis of plasma-type glycoproteins, glycopeptides are prepared by exhaustive pronase digestion and purified by gel filtration chromatography. Final purification is effected by dansylation and thin-layer electrophoresis. The linkage compound 2-acetamido-1-N-β-l-aspartyl-2-deoxy-β-d-glucopyranosylamine is isolated from such glycopeptides as its dansyl derivative following partial acid hydrolysis. Its identity is confirmed by comparison of its properties with those of the synthetic compound. Thus the components of the glycosylamine linkage are identified following complete acid hydrolysis, redansylation, and separation by thin-layer electrophoresis.     

The phylogeny of trypsin-related serine proteases and their zymogens. New methods for the investigation of distant evolutionary relationships.

The sequence of all presently known trypsin-related serine proteases and their zymogens of animal and bacterial origin were optimally aligned on the basis of three different scoring schemes for amino acid comparisons. Sequence homology was found to extend into the activation peptides. The gaps resulting from the alignment of the sequences of the active enzymes formed the basis for a new procedure based on position and number of gaps, which allowed the correct topology of the evolutionary relationship of thrombin and the pancreatic enzymes trypsin, chymotrypsin and elastase to be determined. The procedure was applied in an analogous manner to changes in disulfide bridges as well as to a selected set of amino acid positions.Evolutionary distances between proteins were estimated by minimum, base differences as well as according to the stochastic model of evolution. These distances were used successfully to find the best topology of evolutionary relationships. The fact that the branch lengths in evolutionary trees were less affected by the number of sequences considered when evolutionary distances between contemporary sequences were measured in minimum base differences than when measured according to the stochastic model of evolution, suggested in our specific case, that minimum base differences yielded estimates of evolutionary distance closer to reality than the stochastic model of evolution.All these techniques combined yielded the following picture for the evolution of the four protease families. Prothrombin and the zymogens of the pancreatic serine proteases had a common ancestor with tryptic specificity. After the initial divergence, the gene for trypsinogen duplicated. Evidence was found that the duplicated gene underwent drastic changes for a short period of time to become eventually the common ancestor of chymotrypsin and elastase. The phylogenetic tree elaborated for these enzyme families and the methods introduced to determine its topology, should readily allow determination of the attachment site of branches leading to newly sequenced serine proteases, provided their amino acid sequence can be aligned fairly unambiguously. In addition, the consequences of the alignment of the different serine proteases for the relationship of zymogen to enzyme are discussed.     

Plasmodium knowlesi: In vitro biosynthesis of methionine

Methionine biosynthesis was studied in rhesus monkey erythrocytes infected with Plasmodium knowlesi malaria which were cultured in vitro with l-[3-¹⁴C]serine, methyl-[¹⁴C]tetrahydrofolic acid, and l-[³⁵S]homocysteine. Radioactivity derived from [3-¹⁴C]serine was detected in approximately equivalent amounts in methionine and thymidylic acid by thin-layer chromatography of acid-hydrolysates of washed erythrocytes. The results with methyl-[¹⁴C]tetrahydrofolic acid were inconclusive. Radioactivity from l-[³⁵S]homocysteine also appeared in methionine but the level of homocysteine required for maximal activity was tenfold that of serine. The results indicate that the serine: 5,10-methylenetetrahydrofolic acid: 5-methyl-tetrahydrofolic acid: methionine biosynthetic pathway is present in the P. knowlesi malaria parasite.     

Molecular cloning and sequence analysis of cDNAs coding for a serine proteinase and a Kunitz-type inhibitor in the venom gland of the Vipera nikolskii viper

Serine proteinases and Kunitz-type inhibitors are widely represented in the venoms of snakes belonging to different genera. During the studies of the venoms of snakes inhabiting Russia, we have cloned cDNAs coding for novel proteins of these families. A novel serine proteinase that we named nikobin was identified in the venom gland of the Nikolsky viper. The amino acid sequence of nikobin deduced from the cDNA sequence slightly differs from those of the serine proteinases found in other snakes, displaying 15 unique amino acid substitutions. This is the first serine proteinase from a viper of the Vipera genus for which the complete amino acid sequence has been determined. A cDNA coding for a Kunitz-type inhibitor has also been cloned. The deduced amino acid sequence of the inhibitor displays overall homology to the already known sequences of analogous proteins from vipers of the Vipera genus. However, several unusual amino acid substitutions that can cause a change of the inhibitor activity have been detected.     

The metabolism of serine and glycine in mutant lines of Chinese hamster ovary cells

This report describes studies of mutant lines of cultured Chinese hamster ovary cells that have different levels of serine transhydroxymethylase (EC 2.1.2.1). This enzyme, which splits serine to yield glycine and N⁵,N¹⁰-methylene tetrahydrofolic acid, is found in both the mitochondria and cytosol of these cells (see Chasin et al. (1974) Proc. Nat. Acad. Sci. USA71, 718–722). Our experiments with these mutant lines have established a correlation among the amount of mitochondrial serine transhydroxymethylase, the intracellular glycine concentration, and the extent that exogenous serine increases the glycine pool. Limited amino acid incorporation into protein occurred with all cell lines, but in contrast to the glycine-requiring mutant line 51-11, revertants that no longer required glycine for growth showed increased incorporation when the medium was supplemented with serine. These results indicate that normally the mitochondrial serine transhydroxymethylase together with the intracellular serine concentration regulate the supply of glycine and under certain conditions can control the rate of protein synthesis. Additional experiments with radioactive serine and glycine have shown that the mitochondrial serine transhydroxymethylase regulates the interconversion of these amino acids as well as serine oxidation. Calculations based on the ¹⁴CO₂ produced from l-[¹⁴C]serine by the mutant and parental cell lines indicate that approximately 50% of the serine oxidized is initially converted to glycine and an oxidizable one-carbon unit.     

Chemoattraction of Vibrio fischeri to Serine, Nucleosides, and N-Acetylneuraminic Acid, a Component of Squid Light-Organ Mucus

Newlyhatched juveniles of the Hawaiian squid Euprymna scolopes rapidly become colonized by the bioluminescent marine bacterium Vibrio fischeri. Motility is required to establish the symbiotic colonization, but the role of chemotaxis is unknown. In this study we analyzed chemotaxis of V. fischeri to a number of potential attractants. The bacterium migrated toward serine and most sugars tested. V. fischeri also exhibited the unusual ability to migrate to nucleosides and nucleotides as well as to N-acetylneuraminic acid, a component of squid mucus.     

Analysis of some morphological and biochemical characteristics of the egg of the predaceous bugMacrolophus caliginosus (Het.: Miridae) during embryogenesis

The predaceous bug,Macrolophus caliginosus Wagner (Heteroptera: Miridae) is a biological control agent used in greenhouses in the French Mediterranean region. The egg of this mirid is embedded in plant tissues and all embryonic development occurs in this environment. In order to define an artificial substrate for egg-laying, exchanges of chemical substances between the egg and the host plant were investigated by morphological and biochemical analyses. Egg wet weight doubled throughout embryonic development, while egg dry weight did not vary. The amino acid content of the egg remained stable during embryogenesis. Only aspartic acid, serine and alanine decreased during the first five days of development. It can be concluded that exchanges mainly involved uptake of water by the egg.     

Immunochemical studies on blood groups. Immunochemical properties of B-active and non-B-active blood group substances from horse gastric mucosae and the relative size distributions of oligosaccharides liberated by base-borohydride.

Horse B-active and non-B-active glycoproteins from gastric mucosae are indistinguishable in their precipitating abilities with concanavalin A, anti-BP1, type XIV horse antipneumococcal serum, the lectin from Lotus tetragonolobus and a group 1 anti-I serum, Ma; no Le^a or Le^b activity was found. Each was subjected to catalyzed release of its oligosaccharide chains by 0.05 n NaOH in 1 m NaBH₄. Destruction of serine, threonine and 2-acetamido-2-deoxygalactopyranose (dGalNAc) was associated with production of alanine, α-aminobutyric acid and N-acetyl-d-galactosaminitol, as expected for a carbohydrate to peptide linkage via dGalNAc to serine or threonine. No evidence of basecatalyzed peeling was seen. Bio-Gel P-2 elution patterns of the salt-free oligosaccharides from the two preparations were compared. Unlike results obtained with human ovarian cyst substances, very little material was excluded. The largest-size chains are in the range of deca- or dodecasaccharides, and a reduced octasaccharide was isolated. The four most abundant amino acids in both B-active and non-B-active materials are threonine, serine, proline and glutamic acid, which together account for 60% of the weight of amino acids.     

Glycoproteins from the cell wall of Phaseolus coccineus.

1. The use of a modified sodium chlorite/acetic acid delignification procedure for the solubilization of a hydroxyproline-rich glycoprotein fraction from the depectinated cell walls of Phaseolus coccineus is described. 2. The crude glycoprotein was associated with some pectic material; hydroxyproline and serine were the most abundant amino acids, and arabinose, galactose and galacturonic acid the predominant monosaccharides. 3. The bulk of the hydroxyproline is O-glycosidically substituted with tetra- and tri-arabinofuranosides. From methylation analysis the linkages in these arabinosides could be inferred. 4. Ion-exchange chromatography of the crude glycoprotein gave one major and two minor hydroxyproline-rich fractions, with similar amino acid but different monosaccharide composition. 5. In the major fraction, serine appears to be O-glycosidically substituted with a single galactopyranoside residue that can be removed by the action of alpha-galactosidase but not beta-galactosidase. Removal of arabinofuranoside residues by partial acid hydrolysis greatly enhanced the action of alpha-galactosidase. 6. Methylation followed by carboxy reduction with LiAl2H4 has shown the presence of (1 leads to 4)-linked galacturonic acid in the crude glycoprotein fraction but not in the major fraction from the ion-exchange column. Hence the bulk of the pectic material is not associated with the major glycoprotein component. It is suggested that the glycoprotein is held in the wall by phenolic cross-links. 7. Similarities with the glycopeptide moiety of potato lectin provides further evidence for a class of hydroxyproline-rich glycoproteins with common features.     

The phosphorylated pathway of serine biosynthesis links plant growth with nitrogen metabolism

Because it is the precursor for various essential cellular components, the amino acid serine is indispensable for every living organism. In plants, serine is synthesized by two major pathways: photorespiration and the phosphorylated pathway of serine biosynthesis (PPSB). However, the importance of these pathways in providing serine for plant development is not fully understood. In this study, we examine the relative contributions of photorespiration and PPSB to providing serine for growth and metabolism in the C3 model plant Arabidopsis thaliana. Our analyses of cell proliferation and elongation reveal that PPSB-derived serine is indispensable for plant growth and its loss cannot be compensated by photorespiratory serine biosynthesis. Using isotope labeling, we show that PPSB-deficiency impairs the synthesis of proteins and purine nucleotides in plants. Furthermore, deficiency in PPSB-mediated serine biosynthesis leads to a strong accumulation of metabolites related to nitrogen metabolism. This result corroborates ¹⁵N-isotope labeling in which we observed an increased enrichment in labeled amino acids in PPSB-deficient plants. Expression studies indicate that elevated ammonium uptake and higher glutamine synthetase/glutamine oxoglutarate aminotransferase (GS/GOGAT) activity causes this phenotype. Metabolic analyses further show that elevated nitrogen assimilation and reduced amino acid turnover into proteins and nucleotides are the most likely driving forces for changes in respiratory metabolism and amino acid catabolism in PPSB-deficient plants. Accordingly, we conclude that even though photorespiration generates high amounts of serine in plants, PPSB-derived serine is more important for plant growth and its deficiency triggers the induction of nitrogen assimilation, most likely as an amino acid starvation response.

The phosphorylated pathway of serine biosynthesis is required to synthesize serine for plant growth; and its deficiency triggers an amino acid starvation response by inducing nitrogen assimilation.     

Studies on cytochrome c oxidase, II. The chemical constitution of a short polypeptide from the beef heart enzyme.

A low molecular weight (approximately 6000) polypeptide fraction was isolated from beef heart cytochrome c oxidase, consisting of three peptides with the N-terminal end groups isoleucine, phenylalanine and serine. The complete amino acid sequence of the serine component is described. From the chemical constitution, a site-specific cleavage from a precursor protein and a possible function in membrane penetration and complex formation of the oxidase is inferred.     

Chemical composition and rate of synthesis of the larval salivary secretion of the fly Rhynchosciara americana

The salivary secretion of Rhynchosciara americana was chemically analysed. The secretion shows a yellow colour, with a pH of 7·5 and protein as its major component (94·5 per cent of the secretion dry weight). Carbohydrates are minor components of the secretion which amount to 3·4 per cent of the secretion dry weight, of which 2·3 per cent are neutral carbohydrates and 1·1 per cent are galactosamine. The major amino acids present in the secretion proteins are aspartic acid, glycine, serine, and glutamic acid. The salivary secretion proteins can be separated into eleven protein fractions by urea-acrylamide gel electrophoresis from which nine fractions are PAS positive. The salivary pigment moves together with the protein fraction No. 8, which is quantitatively the most important one, and has spectral characteristics identical to a haemolymph pigment. The higher rate of gland protein labelling by ¹⁴C-phenylalanine determined in vivo and in vitro occurs around the middle of the spinning stage at the same time as the appearance of the large chromosomal puffs. The rôle of the salivary secretion in cocoon production is discussed.     

Thiol and disulphide contents of hen ovalbumin. C-Terminal sequence and location of disulphide bond

1. The thiol and disulphide contents of hen ovalbumin were investigated by p-chloromercuribenzoate titration, by determination of cysteic acid content after performic acid oxidation, by measurement of uptake of radioactive iodoacetic acid, and by assay of S-aminoethylcysteine after reaction with ethyleneimine. All results showed that ovalbumin had 6 half-cystine residues. Experiments with and without reducing agents demonstrated that there were 4 thiol groups and 1 disulphide bond. 2. A peptide containing equimolar amounts of S-carboxymethyl-cysteine, serine, valine and proline, but no lysine or arginine, was obtained by radioactive labelling of the cysteine residues with iodo[¹⁴C]acetic acid followed by electrophoretic and chromatographic separation of tryptic digests. It was concluded that the C-terminal sequence of ovalbumin is -Cys-Val-Ser-Pro. 3. The location of the disulphide bond was studied by using a double-labelling technique. It was shown that one end of the disulphide was located in this C-terminal peptide.