Evidence for covalent binding between phosphopeptides and terminal deoxynucleotides in highly purified calf thymus DNA

Summary Highly purified DNA from calf thymus nuclei (N-DNA) was found to cleave after reaction with a chelating agent and subsequent dialysis. During the cleavage phosphopeptides (PPs) were released into the dialysates. At the end of the cleavage, approximately one half of the PP material remained with the DNA. Since it was so strongly bound, it was considered to be retained in the DNA structure by covalent bonding. In order to confirm this, a commercial DNA (S-DNA) was ultrasonicated and digested with pancreatic DNAase, exonuclease III, and S1 nuclease. DEAE Sephacel chromatography of the digested material yielded 5 fractions. The fraction 2, having the highest proportion of proteinaceous material, was digested with Pronase. Amino acid analysis of the hydrolysis mixture yielded phosphoserine (Pser), asp, thr, ser, glu, gly, ala, val, ile, leu, and arg. The mixture was chromatographed again on DEAE Sephacel. From this a single fraction, number 5, was found to contain both deoxynucleotides and the amino acids, Pser, asp, ser, glu, and gly in a molar ratio of > 7:3:2:2:5. The mixture obtained by hydrolysis of this fraction with snake venom diesterase was again chromatographed on DEAE Sephacel. This fractionation gave two main peaks, one corresponding to the same 5 amino acids and the other to deoxynucleotide material. From this it was concluded that the fraction used for diesterase digestion consisted of deoxynucleotide-amino acids, with covalent diester bonds between the deoxynucleotide and amino acid portions.Dedicated to Prof. L.E. Feinendegen on the occasion of his 60th birthday     

Characterization of phosphopeptides released during dialysis of EDTA-reacted highly purified DNA prepared from calf thymus nuclei

The treatment of highly purified DNA obtained from calf thymus nuclei (N-DNA) with a chelating agent and subsequent repeated dialyses led to release of phosphopeptides (PPs) into the dialysates. By means of anion exchange column chromatography, the PPs were separated into 9 main fractions. Two of them (P1 and P5) contained the amino acids phosphoserine, asp, thr, ser, glu, gly, ala, val, ile, leu, and arg, as well as metal ion complexes of phosphoserine. The complexes were dissociated by deionization with nitrilotriacetate + Chelex. The proportion of phosphoserine was about twice as great in P5 as in P1. Whereas P1 and P5 contained essentially no nucleotide material, the other fractions contained ribonucleotides and deoxynucleotides. The deoxynucleotide content was less than 10% of that of total nucleotides. After a deionizing treatment, the amounts of nucleotides in these fractions were reduced to a level corresponding to 1 nucleotide per peptide of 5-15 amino acids.     

Schistosoma mansoni: incorporation and metabolism of protein amino acids in vitro

1. The amino acid composition of total proteins in six stages of the life cycle of Schistosoma mansoni was determined by routine autoanalysis of acid hydrolysates. Aspartate, glutamate and glycine were consistently the most abundant protein amino acids in all stages. 2. Incorporation of each of the protein amino acids into adult and egg proteins was determined using 72 hr cultures in complex media. Incorporation rates varied widely and there was no correlation between abundance in protein and the rate of incorporation. 3. Only five amino acids were interconverted to other amino acids which were themselves incorporated into worm and egg proteins (ala, arg, asp, gly, ser); of these only two (glu from ala and pro from arg) appeared to be of quantitative significance. Exogenous glucose yielded only three protein amino acids (ala, asp, glu). 4. The data are considered in the light of differences in egg and adult protein synthesis and with particular regard to potential chemotherapy at this level.     

Relationship between bound and free amino acids in the brain of growing rats]

Total pool of glutamate, glutamine and GABA in the hemispheres increases during postnatal life of rats, the increase being due to that in free and bound forms of amino acids. In the cerebellum of 1-day rats, the content of free and bound glu, gln asp, GABA, bound ala and free gly is lower, whereas the level of free glu and ala, bound gly is higher than in mature animals. To the end of the 1st week, total amino acid content decreases, except GABA, which is increased. Aminon acid content begins to increase at the 21th and 28th days of postnatal life.     

Behavioural responses of glass eels (Anguilla anguilla) towards amino acids

The behavioural responses of glass eels of Anguilla anguilla towards amino acids were investigated by binary choice experiments testing different concentrations of 14 L-amino acids in fresh water and salt water. Glass eels responded to solutions of individual amino acids down to a concentration of 10⁻⁸M, 10⁻⁹m. Media of different salinities influenced the responses. In freshwater, gln and thr were strongly attractive; asn, ala, met, glu and ile induced significant avoidance; gly elicited multimodal reactions depending on concentrations; his, lys, phe, val, leu and asp hardly influenced behaviour. In salt water, only gly, asn and lys significantly influenced the behaviour of the glass eels.     

Amino acid analysis of proteins and tightly bound phosphopeptides in calf thymus DNA: indications of a novel regulatory mechanism

Purification of DNA prepared from calf thymus nuclei, which were isolated at temperatures of -10 degrees to -15 degrees C, termed N-DNA, reduced the protein content from 17% to 0.7%. Amino acid analysis of the crude N-DNA revealed that the protein material removed in this process contained lys and phe, whereas in purified N-DNA neither of these amino acids was present. The crude N-DNA had a lower total Pser molar ratio (5.9) than that of the purified N-DNA (22.6). The purification also effected a large decrease of molecular weight, from 170 to 15 million daltons, roughly corresponding to the size of replicons. The amino acid composition of the N-DNA was compared with those of the two PP fractions, a) the PPs released into the dialysates, and b) the core material bound in the DNA, probably covalently, after reaction of N-DNA with EDTA and subsequent dialysis. N-DNA had an intermediate total Pser molar ratio between that of a) (35.3) and b) (11.9). Analysis of a standard preparation of DNA (S-DNA), which involved initial rupture of nuclei in the presence of cytoplasmic components, gave elevated values of asp and glu, a total Pser average value of 8.7 before, and 9.0, after the purification, and again phe and lys in the crude DNA.     

A computational model of mitochondrial deoxynucleotide metabolism and DNA replication

We present a computational model of mitochondrial deoxynucleotide metabolism and mitochondrial DNA (mtDNA) synthesis. The model includes the transport of deoxynucleosides and deoxynucleotides into the mitochondrial matrix space, as well as their phosphorylation and polymerization into mtDNA. Different simulated cell types (cancer, rapidly dividing, slowly dividing, and postmitotic cells) are represented in this model by different cytoplasmic deoxynucleotide concentrations. We calculated the changes in deoxynucleotide concentrations within the mitochondrion during the course of a mtDNA replication event and the time required for mtDNA replication in the different cell types. On the basis of the model, we define three steady states of mitochondrial deoxynucleotide metabolism: the phosphorylating state (the net import of deoxynucleosides and export of phosphorylated deoxynucleotides), the desphosphorylating state (the reverse of the phosphorylating state), and the efficient state (the net import of both deoxynucleosides and deoxynucleotides). We present five testable hypotheses based on this simulation. First, the deoxynucleotide pools within a mitochondrion are sufficient to support only a small fraction of even a single mtDNA replication event. Second, the mtDNA replication time in postmitotic cells is much longer than that in rapidly dividing cells. Third, mitochondria in dividing cells are net sinks of cytoplasmic deoxynucleotides, while mitochondria in postmitotic cells are net sources. Fourth, the deoxynucleotide carrier exerts the most control over the mtDNA replication rate in rapidly dividing cells, but in postmitotic cells, the NDPK and TK2 enzymes have the most control. Fifth, following from the previous hypothesis, rapidly dividing cells derive almost all of their mtDNA precursors from the cytoplasmic deoxynucleotides, not from phosphorylation within the mitochondrion. simulation; nucleotide phosphorylation; nucleoside transport; mitochondrial DNA     

Variations circadiennes des acides aminés libres de l'hemolymphe de Penaeus japonicus

The non-essential free amino acids of Peneaus japonicus hemolymph (asp, ser, glu, pro, gly, tyr, arg, ala, cys, tau) are more common than the essential ones: 750 pmol μl^?1 of hemolymph vs 330 pmol. Under a light-dark (L-D); 12-12 photoperiod, tricircadian variations of males or tetracircadian variations of females are more pronounced for non-essential amino acids then for essential ones. In the first case, free amino acid concentrations of hemolymph can be multiplied by a factor of three, and in the second case by a factor of six; but circadian variations of females are greater than those of males. Differences between the maximum and minimum of essential free amino acid concentrations of male and female hemolymph are more frequent than for non-essential amino acids. A differences of 2 h between the minimum of essential and non-essential amino acid concentrations in males only appeared during the afternoon. The more concentrated free amino acids in P. japnicus hemolymph are glycine, proline, histidine, and alanine; the less concentrated are lysine, cysteine and glutamic acid while others, like leucine, isoleucine, phenylalanine and tyrosine can only be estimated at 10.00 and 24.00 h.     

兔阑尾中一种新的21kD的钙结合蛋白的纯化与鉴定

纯化与鉴定了Ｂ淋巴细胞中一种新的分子量为２１ｋＤ的钙结合蛋白（ＣａＢＰ２１）。兔阑尾淋巴细胞匀浆经热变性,Ｐｈｅｎｙｌ－Ｓｅｐｈａｒｏｓｅ与ＤＥＡＥ－Ｓｅｐｈａｒｏｓｅ柱层析,自每１ｋｇ细胞沉积物中获得ＳＤＳ－ＰＡＧＥ均一的ＣａＢＰ２１５．３ｍｇ。ＨＣｌ水解后的酸性氨基酸（Ａｓｐ＋Ｇｌｕ）含量为２６％。如同大多数钙结合蛋白一样,Ｎ末端封闭阻止其进行Ｅｄｍａｎ降解。ＣａＢＰ２１中疏水性氨基酸（计Ｇｌｙ,不计Ｔｒｐ）约占４６％,碱性氨基酸１０％,酸性氨基酸与极性氨基酸约４４％。ＣａＢＰ２１有较高的Ｓｅｒ、Ｔｙｒ含量。肽谱分析等确证ＣａＢＰ２１为２个相同或相似亚基二聚体。以ＡｒｓｅｎａｚｏⅢ作Ｃａ２＋结合分析表明每分子ＣａＢＰ２１可结合４分子Ｃａ２＋,对Ｃａ２＋的结合常数约为１０－５ｍｏｌ／Ｌ。各种性质表明ＣａＢＰ２１是一种不同于其他已知钙结合蛋白的新钙结合蛋白。     

Purification of a syngeneic cross-reactive autotumorolytic factor

An autotumorolytic fraction (ATF) derived from sera of mice bearing spontaneous mammary adenocarcinoma has been purified by sequential chromatography on Sephacryl 200 SF, DEAE Sephacel, hydroxylapatite, and Sephacryl 200 SF. At each stage of the purification, tumorolytic activity was assessed by the ability of the active material to induce lysis of a 2-week-old mammary tumor, and verified by histopathological analysis. Active fractions obtained during the stages of purification were capable of inducing lysis of tumors in both the original donor mice and the syngeneic tumor-bearing mice. Lytic activity was specific only for tumor tissue. This syngeneic crossreactivity of partially purified materials permitted pooling of serum samples for purification purposes. The resultant final preparation of ATF is an homogenous protein fraction, as verified by gradient SDS-polyacrylamide gel electrophoresis (SDS-PAGE) and high-performance liquid chromatography. The molecular weight of active ATF is approximately 50,000 Da, as determined by gradient SDS-PAGE.     

THE IN VITRO FORMATION OF ACETYL-ASPARTYL-PEPTIDO-SEROTONIN COMPLEXES BY PIG HYPOTHALAMIC TISSUE EXTRACTS

Peptido-serotonin complexes are formed on incubation of pig hypothalamic tissue extracts with acetyl-aspartate, the amino acids glu. ser, gly and ala. an ATP-regenerating system and serotonin. The purification and partial characterisation of two acetyl-aspartyl-peptido-serotonin complexes is described.     

Cell wall composition and deoxyribonucleic acid similarities among the anaerobic coryneforms, classical propionibacteria, and strains of Arachnia propionica

Eighty strains of anaerobic coryneforms were compared with 29 strains of classical propionibacteria and 8 strains of Arachnia propionica by cell wall analysis, deoxyribonucleic acid (DNA) base compositions, and nucleotide sequence similarities. The anaerobic coryneforms have DNA base compositions in the range of 58 to 64% guanine + cytosine (GC) and show at least three homology groups. The largest group corresponds to organisms identified as Propionibacterium acnes and shows about 50% homology to strains in the P. avidum homology group. The third group, P. granulosum, shows low levels of similarities to the other two. All strains of anaerobic coryneforms have some combination of galactose, glucose, or mannose as cell wall sugars, and most have alanine (ala), glutamic acid (glu), glycine (gly), and l-alpha-epsilon-diaminopimelic acid (l-DAP) as amino acids of peptidoglycan. However, a few strains in the P. acnes and P. avidum homology groups have meso-DAP and minimal amounts of glycine. Two serological types, based on cell wall antigens, were found in the P. acnes homology group. One type had galactose, glucose, and mannose as cell wall sugars, the other glucose and mannose only. The classical propionibacteria have DNA base compositions in the range of 65 to 68% GC and show four homology groups which correspond closely to van Niel's classification as given in the 7th edition of Bergey's Manual. The P. jensenii group showed about 50% homology to the P. thoenii group and about 30 to 35% to the P. acidi-propionici group. The P. freudenreichii strains showed a rather lower level of similarity (8 to 25%) to the other homology groups. Most of the strains of classical propionibacteria also have some combination of galactose, glucose, or mannose as cell wall sugars and ala, glu, gly, and l-DAP as peptidoglycan amino acids, but P. shermanii and P. freudenreichii strains, which form a single homology group, have galactose, mannose, and rhamnose as cell wall sugars and ala, glu, and meso-DAP in their peptidoglycan. There is a rather low level of DNA homology (10 to 20%) between the anaerobic coryneforms and classical propionibacteria. However, the strains of A. propionica which have a GC content of 64 to 65% and form a single homology group, show no homology to either of the other two major groups.     

Solubilization and partial purification of squalene synthase from daffodil microsomal membranes

A squalene synthase was solubilized from daffodil (Narcissus pseudonarcissus L.) microsomes with CHAPS, a zwitterionic non-denaturating detergent. By successive chromatography on DEAE Sephacel and APP Sepharose a fraction enriched in this enzyme (21-fold) was prepared.     

绿色木霉LTR-2 β-1, 3-葡聚糖酶基因的克隆及其在 毕赤酵母中的表达

根据从GenBank中检索到的木霉菌β-1,3-葡聚糖酶基因序列设计引物,以高产β-1,3-葡聚糖酶菌株--绿色木霉LTR-2的cDNA为模板,采用PCR方法扩增得到内切β-1,3-葡聚糖酶基因(glu).将glu克隆至载体pMD18-T上,进行了全序列测定.序列分析表明该基因由2289个核苷酸残基组成,含有一个开放阅读框架,可以编码762个氨基酸,与报道基本相同.翻译后的氨基酸序列含有两个β-1,3-葡聚糖酶的保守区RVVYIPPGTY和AASQNKVAYF.基因与已发表的木霉β-1,3-葡聚糖酶基因有较高的同源性,其中和哈茨木霉bgn3.1和绿木霉bgn13.1的同源性达到93%.序列已经提交GenBank,登录号为EF176582.将glu基因插入到巴斯德毕赤酵母(Pichia pastoris)穿梭载体pPIC9K中,获得重组质粒pGLU14,经线性化后转化毕赤酵母菌株KM71.经大量平板筛选,获得能有效分泌表达β-1,3-葡聚糖酶的毕赤酵母工程菌株KGLU14,菌落PCR扩增证实了glu基因已经整合到酵母基因组中.SDS电泳结果表明其β-1,3-葡聚糖酶的分子量大约为80kDa,和理论推测值大致相同.摇瓶发酵结果表明,培养基中β-1,3-葡聚糖酶的活力可达889U/mL.     

A unifying concept for the amino acid code

The structure of the genetic code is related to a Gray code, which is a plausible theoretical model for an amino acid code. The proposed model implies that the most important factor in shaping the code was the effects of mistakes in translation, not effects of mutations. Another possible implication is that the preservation of stiffness and flexibility at appropriate places in a protein chain is as important in protein structure as the appropriate placement of hydrophilic (external) and hydrophobic (internal) residues. Other results are a simple conceptualization of the relationships among the 20 amino acids and their relations to their codons. The detailed relationships are summarized in the following ‘similarity alphabet’: ala, thr, gly, pro, ser; asp, asn, glu, gln, lys; his, arg, trp, tyr, phe; leu, met, ile, val, cys; (ATGPS DNEQK HRWYF LMIVC in the one-letter code). This alphabet falls into four groups of amino acids: small, external, large, internal. The approximate relation of the groups to their codons is expressed as: the first base of a codon controls size—a purine means a small amino acid, a pyrimidine means large; the middle base controls cloisterednes—purine means external, pyrimidine means internal. These relationships express the minimum change principle upon which the code appears to be founded.     

Cyclic AMP stimulated protein kinase activity within the secretory vesicle fraction of rat islets.

The isolated rat islet secretory vesicle fraction (24,000xg) was incubated with gamma [³²P ATP] and the TCA-insoluble material was pelleted. The pellet was acid hydrolyzed, lyophilized, redissolved, then subjected to two-dimensional chromatographic separation. Two labeled compounds were identified, i.e., phosphoserine and inorganic phosphorus. With the addition of cyclic AMP (3.5 × 10^?6M), there was a 235% increase in phosphoserine radioactivity (P<.01) within endogenous protein subunits. When histones were added to the incubation media, the addition of cyclic AMP resulted in a threefold increase in phosphoserine radioactivity in the TCA-insoluble material (P<.01). A comparison was made of cyclic AMP-stimulated protein kinase activity in the homogenate and various islet subcellular fractions. Cyclic AMP-stimulated protein kinase activity is associated with the 24,000xg (secretory vesicle) fraction.     

Extraction and purification of tissue phosphopeptides

We describe a method of extraction and partial purification of phosphopeptides isolated from pig brain or from the electrical organ of Torpedo marmorata. The extraction of the phosphopeptides was achieved by alcoholic 0,04 N potassium hydroxyde solution or by 10(-1) M KCL containing 10(-3) M EDTA and 10(-4) M DTT. After having tried various fractionation methods like ion exchange chromatography or gel filtration we chose chromatography on DEAE Sephadex followed by purification of the isolated fractions by Sephadex G 25 filtration. The most important phosphate fractions (one was purified to about 90 per cent) were characterized by the determination of the N/P ratio which was different from one phosphopeptide to another. The amino acid composition showed a high glycin, serine and "acid" amino acid content.The presence of phosphoserine was shown by electrophoresis and chromatography of a partial hydrolysate of in vivo 32P labelled phosphopeptides isolated from rat liver. The polyanionic structure of these phosphopeptides allow them to act as real ion exchangers which might be involved during active transport mechanisms in cellular membranes.     

The isolation and partial characterization of low-molecular-weight phosphorylated component of the non-histone proteins of mouse nuclei.

After labelling of mouse liver nuclei with [gamma-32P]ATP in vitro, 10-20% of the radioactivity incorporated into the saline-soluble nuclear and HAP2 chromatin fractions was located in a low-molecular-weight component (component 10) with pI near 4.5 in urea. By using combinations of ion-exchange chromatography, preparative thin-layer isoelectric focusing and gel filtration, this component was isolated from both nuclear fractions. Recovery from the saline-soluble fraction was poor under conditions that allow endogenous phosphatases to be active. Component 10 was shown to be a phosphoprotein on the basis of enzyme-digestion experiments and the detection of phosphoserine and phosphothreonine. The 32P radioactivity did not appear to be associated with phosphorylated basic amino acids. Its molecular weight was determined by gel chromatography and electrophoresis in sodium dodecyl sulphate/polyacrylamide gels as approx. 10000, and tryptic digestion of the reduced carboxymethylated protein in urea yielded two 32P-labelled peptides. It has not been possible as yet to assign a function to component 10, though its similarity to other low-molecular-weight acidic proteins is discussed.     

Properties of glutathione peroxidase isolated from human plasma

Human plasma glutathione peroxidase (GPx) was purified to homogeneity by ammonium sulfate fractionation, gel filtration on Sephadex G-150, chromatography on DEAE Sephacel, chromatofocusing with polybuffer, and gel filtration with Sephadex G-75. This isolation resulted in about 5,400-fold purification of the enzyme with a 32% yield in enzyme activity. The final preparation had a specific activity of about 28 units (mmoles NADPH oxidized) per milligram of protein. Determination of selenium on the purified enzyme revealed a content of 3.8 g atoms per mole GPx. Gel electrophoresis using SDS with standard proteins revealed a molecular weight of about 23,000 for the subunits, which would indicate a molecular weight of about 92,000 for the native enzyme. Amino acid analyses of the purified GPx indicated aspartate, glutamate, proline, glycine, alanine, and leucine as the predominant amino acids and cysteine, methionine, tryptophan, and histidine as the minor amino acids.