Lipid-saccharide intermediates in glycoprotein biosynthesis. I. Formation of an oligosaccharide-lipid by thyroid slices and evaluation of its role in protein glycosylation

The synthesis of oligosaccharide-lipids thought to play a role in the attachment of carbohydrate to protein has been studied in incubations of slices from calf kidney, pancreas, thymus, and liver, as well as from hen oviduct. These compounds were characterized after radiolabeling of their saccharide moiety by incubation with [14C]glucose or [14C]mannose and a comparison was made with the oligosaccharide-lipid produced by thyroid slices. Furthermore, the unlabeled glycolipid was prepared from hen oviduct for the purpose of quantitating its sugar constituents. Purification of the oligosaccharide-lipids extracted with chloroform/methanol/water (10/10/3) was achieved by DEAE-cellulose chromatography and their carbohydrate moieties were released by mild acid hydrolysis. On the basis of gel filtration it was determined that the lipid-bound oligosaccharides formed by oviduct, thymus, kidney, and liver had molecular weights comparable to that from thyroid (about 2400). The saccharide moiety of the glycolipid from pancreas was however distinctly smaller in size with a molecular weight of approximately 1800. Analyses of the radiolabeled oligosaccharide-lipids from oviduct, kidney, and thymus indicated that they, like the compound from thyroid slices, but unlike those believed to be formed by cell-free systems from various tissues, contained glucose in addition to mannose and N-acetylglucosamine as their monosaccharide constituents. This compositional data was supported by the finding that the unlabeled oligosaccharide from oviduct consists of 10 mannose, 1 glucose, and 2 N-acetylglucosamine residues. Sodium borohydride reduction of this oviduct saccharide moiety indicated that 1 of the 2 glucosamines was situated in a reducing terminal position. The radiolabeled oligosaccharide from the glycolipid produced by pancreas differed from the others analyzed in that it contained only trace amounts of glucose. Upon treatment with alpha-mannosidase this glucose-deficient pancreatic oligosaccharide was extensively digested (85% of the mannose released). In contrast, the carbohydrate moieties of oviduct, kidney, and thymus, like that of thyroid, underwent a more limited digestion with the alpha-mannosidase (55% or less of the mannose released) suggesting that the presence of glucose may serve to block a more complete degradation of these oligosaccharides by this enzyme.     

Translation of ovalbumin mRNA in Xenopus laevis oocytes. Characterization of the system and effects of estrogen on injected mRNA populations

Ovalbumin messenger RNA (mRNAov) purified from hen oviduct was injected into Xenopus laevis oocytes. The oocytes were incubated in culture medium containing [3H]leucine. Analysis of the oocyte cytosol on Sephadex G-15O columns demonstrated a peak of radioactivity which cochromatographed with authentic ovalbumin. Radioactive protein contained in this peak was precipitated by ovalbumin antiserum, coelectrophoresed with ovalbumin on sodium dodecyl sulfate (SDS) and urea gels at pH 8.7, and eluted with the protein at the same pH (4.8) on CM-cellulose chromatography. Injection of increasing amounts of mRNAov was found to elicit a linear response in terms of ovalbumin synthesis. Moreover, there was linear incorporation of radioactivity into microinjected oocytes over a minimum period of 91 h. Less than 1 ng mRNAov was detected in this system. Ovalbumin mRNA activity was present in RNA preparations from chicks treated with estrogen but was undetectable in animals withdrawn from the hormone. This study constitutes an initial demonstration of a steroid hormone-induced alteration in mRNA population as assayed in intact viable heterologous cells.     

Evidence that vitamin A is not required for the biosynthesis of ovalbumin in chicks

Four-day-old pullets fed a vitamin A-deficient diet were stimulated daily with 1 mg 17beta-estradiol-3-benzoate/day for 6 to 19 days. The onset of vitamin A deficiency had no effect on oviduct growth in these chicks; even though vitamin A-deficient chicks showed a severe decline in growth rate while controls (fed the same diet supplemented with retinyl palmitate) continued to grow, estrogen stimulated resulted in similar oviduct size. Ovalbumin concentrations of estrogen-stimulated chicks were determined by immunoprecipitation of the soluble protein supernatant fraction of oviduct. The concentration of ovalbumin in oviducts of chicks fed a vitamin A-supplemented diet was similar in the concentration in oviducts of chicks fed a vitamin A-deficient diet. The incorporation of [3H]glucosamine and 14C-amino acids into immunoprecipitable ovalbumin, following the in vitro incubation of minced oviduct, indicated that ovalbumin synthesis was not affected by vitamin A deficiency. The specific activity of incorporated [3H]glucosamine, the 14C-amino acid incorporation into ovalbumin, the relative rate of ovalbumin synthesis, and the relative effiency of [3H]glucosamine incorporation into ovalbumin were each similar between the two diet groups. The relative efficiency of [3H]glucosamine incorporation into sodium dodecyl sulfate and dithiothreitol extractable membranous proteins of oviduct was not affect by vitamin A deficiency.     

The distribution of nascent polypeptide chains among intact polyribosomes from Chlamydomonas reinhardi

A model of polyribosome function based on tape theory has been applied to the analysis of intact polyribosomes from Chlamydomonas reinhardi. The distribution of nascent polypeptide chains found on polyribosomes does not conform to the expected pattern in which small polypeptides are synthesized on small polyribosomes and large polypeptides on correspondingly large polyribosomes. This discrepancy was revealed in the analysis of specific activity of polyribosomes (radioactivity in nascent chains per ribosome) versus polyribosome size at labeling saturation. It was found that the specific activity of small polyribosomes was higher than predicted and that of large polyribosomes was lower. This finding was validated by measuring the sizes of nascent chains from various polyribosome size classes by sodium dodecyl sulfate (SDS)-polyacrylamide gel electrophoresis. The presence of large polypeptides on small polyribosomes could be partially accounted for by the synthesis of polypeptides on chloroplast (chloramphenicol-sensitive) polyribosomes. A maximum peptide interval time of 10 s was estimated from the labeling kinetics of the nascent chains of mid-sized (cytoplasmic) polyribosomes. This rate of translation is comparable to that reported in other eucaryotic cells.     

The 70 carboxyl-terminal amino acids of nascent secretory proteins are protected from proteolysis by the ribosome and the protein translocation apparatus of the endoplasmic reticulum membrane

We have used proteolysis to examine the environment through which nascent secretory proteins are translocated across the membrane of the endoplasmic reticulum. After solubilization of rough microsomes with detergent, fragments comprised of the approximately 70 carboxyl-terminal amino acids of translocating nascent chains initiated and targeted in vivo were protected from digestion by added proteases. About 40 amino acids of nascent chains were protected from proteolysis by the ribosome; thus, membrane-derived components protect an additional 30 amino acids. Under conditions in which those 30 additional amino acids are protected, only a small set of integral membrane proteins remained associated with the ribosome. These proteins include the Sec61 complex previously identified as the core component of the membrane-bound protein translocation apparatus. These results support the concept of a translocation pore that makes intimate contact with the ribosome and thereby protects nascent chains from proteolytic digestion for an additional, constant length.     

Interactions of ribosome nascent chain complexes of the chloroplast-encoded D1 thylakoid membrane protein with cpSRP54

The mechanisms of targeting, insertion and assembly of the chloroplast-encoded thylakoid membrane proteins are unknown. In this study, we investigated these mechanisms for the chloroplast-encoded polytopic D1 thylakoid membrane protein, using a homologous translation system isolated from tobacco chloroplasts. Truncated forms of the psbA gene were translated and stable ribosome nascent chain complexes were purified. To probe the interactions with the soluble components of the targeting machinery, we used UV-activatable cross-linkers incorporated at specific positions in the nascent chains, as well as conventional sulfhydryl cross-linkers. With both cross-linking approaches, the D1 ribosome nascent chain was photocross-linked to cpSRP54. cpSRP54 was shown to interact only when the D1 nascent chain was still attached to the ribosome. The interaction was strongly dependent on the length of the nascent chain that emerged from the ribosome, as well as the cross-link position. No interactions with soluble SecA or cpSRP43 were found. These results imply a role for cpSRP54 in D1 biogenesis.     

Use of ionizing radiation to prevent restenosis in interventional cardiology

It is well known that the expression of carbohydrate chains on cell changes during the development and progression of carcinoma. Some carbohydrate chains have been used in clinical practice as tumor markers. Some, such as sialyl Lewis a (CA 19.9), sialyl Lewis X, and Tn, are known to function as adhesion molecules. However, their role in the development of hematogenous metastasis is still controversial. In this paper, many investigations concerning this issue are reviewed. Clinical trials for treatment of patients with advanced cancer using carbohydrate chains are also mentioned.     

The nascent polypeptide-associated complex modulates interactions between the signal recognition particle and the ribosome

BACKGROUND: The first step in the co-translational targeting of secretory proteins to the endoplasmic reticulum membrane involves the recognition of signal sequences by the 54 kDa subunit of the signal recognition particle (SRP) as they emerge from the ribosome. It has recently been proposed that the nascent polypeptide-associated complex (NAC) contributes to the fidelity of targeting by modulating interactions that occur between the ribosome-nascent chain complex, the SRP and the endoplasmic reticulum membrane. Precisely how NAC influences SRP function is presently unclear. RESULTS: We have used immunoblotting experiments to monitor interactions between the SRP and the ribosome-nascent chain complex, in the absence and presence of NAC. In the absence of NAC, SRP binds in a high-salt-resistant manner only to ribosomes that contain a signal sequence, confirming the specificity of SRP for signal sequences. Binding of SRP to signalless ribosome nascent chains is observed at lower salt concentrations; however, the amount of SRP bound to this complex is indistinguishable from that bound to ribosomes lacking nascent chains. Thus, this salt-sensitive binding is likely to be the result of interactions between SRP and the ribosome that occur independently of the nascent chain. A minimal particle consisting of SRP54 and SRP RNA is sufficient to confer salt-resistant binding to ribosomes that contain signal sequences, whereas all of the SRP subunits are required for salt-sensitive binding to ribosomes that lack nascent chains. This salt-sensitive binding by SRP is inhibited by the addition of purified NAC. CONCLUSIONS: Based on our results, we define two distinct modes of interaction between SRP and the ribosome-nascent chain complex: salt-resistant interactions between SRP54 and signal sequences, and salt-sensitive interactions between additional components of SRP and the ribosome. We conclude that NAC does not directly influence signal sequence recognition by SRP but, rather, that it negatively modulates interactions that occur between SRP and the ribosome itself. These results are discussed in terms of a model wherein SRP and NAC regulate each others' activity during protein targeting.     

Identifying the glycosylation sites and site-specific carbohydrate heterogeneity of glycoproteins by matrix-assisted laser desorption/ ionization mass spectrometry

A sensitive and facile method is described to identify the glycosylation sites and site-specific heterogeneity in the carbohydrate attached to glycoproteins. In this procedure, the peptide backbone of the glycoprotein is cleaved enzymatically. The resulting peptide/glycopeptide mixture is divided into three fractions. The first is analyzed directly by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS), while the other two aliquots are analyzed by MALDI-MS after enzymatic release of the N-linked chains and the N- and O-linked chains. Comparison of these MALDI mass spectra provides the molecular weight of each carbohydrate side chain and of the peptide to which it was attached. This information combined with the amino acid sequence of the protein identifies the glycosylation sites, and provides information concerning site-specific oligosaccharide heterogeneity. This approach does not require time-consuming liquid chromatographic separations and can be performed on as little as 10 pmol of glycoprotein. Thus, our approach is faster and simpler than procedures currently used for glycosylation site mapping, and may offer a slight sensitivity advantage.     

The carbohydrate moiety of alpha-galactosidase from Trichoderma reesei

Alpha-galactosidase from Trichoderma reesei is a glycoprotein that contains O- and N-linked carbohydrate chains. There are 6 O-linked glycans per protein molecule that are linked to serine and threonine and can be released by beta-elimination. Among these are monomers: D-glucose, D-mannose, and D-galactose; dimers: alpha1-6 D-mannopyranosyl-alpha-D-glycopyranoside and alpha1-6 D-glucopyranosyl-alpha-D-galactopyranoside and one trimer: alpha-D-glucopyranosyl-alpha1-2 D-mannopyranosyl-alpha1-6 D-galactopyranoside. N-linked glycans are of the mannose-rich type and may be released by treating the protein with Endo-beta-N-acetyl glycosaminidase F or by hydrozinolysis. The enzyme was deglycosylated with Endo-beta-N-acetyl glycosaminidase F as well as with a number of exoglycosidases that partially remove the terminal residues of O-linked glycans. The effect of enzymatic deglycosylation on the properties of alpha-galactosidase has been considered. The effects of tunicamycin and 2-deoxyglucose on the secretion and glycosylation of the enzyme during culture growth have been analysed. The presence of two glycoforms of alpha-galactosidase differing in the number of N-linked carbohydrate chains and the microheterogeneity of the carbohydrate moiety of the enzyme are described.     

Carbohydrate-carbohydrate interactions in adhesion

Cell-cell interactions play an important role in the development, maintenance, and pathogenesis of tissues. They are highly dynamic processes which include migration, recognition, signaling, adhesion, and finally attachment. Cells on their pathway to a final location have to pass and interact with their substratum formed of matrix and cell layers. Testing and recognition are important keys for the proper result of tissue formation. They can, however, also lead to diseases when they are misused in pathological situations, by microorganisms or malignant cells, for instance. Carbohydrates, which are the most prominent surface-exposed structures, must play an important role as recognition molecules in such processes. The rich variability of carbohydrate sequences which cell surfaces can present to lectins, adhesion molecules, and other ligands creates a refined pattern of potential attachment sites. The subtle control of the surface presentation density can provide variations in attachment strength. Not only the carbohydrate sequences but also the fact that carbohydrates can be branched while proteins cannot and that the oligosaccharide chains can be attached to the protein backbone in different densities and patterns will create yet more interaction possibilities. Maximal use of the combinatorial richness of carbohydrate molecules would be made when carbohydrate sequences could interact with other carbohydrate sequences. Such interactions have only very rarely been considered for biochemically and biologically relevant situations since they are difficult to measure. A few are known and will be summarized here with the hope that this wealth of possible chemical interactions may be considered more and more by surface cell biochemists when analyzing fine tuning in cellular interactions.     

Structural studies of the sugar chains of hen ovomucoid. Evidence indicating that they are formed mainly by the alternate biosynthetic pathway of asparagine-linked sugar chains

The carbohydrate moieties of hen ovomucoid were released as oligosaccharides by hydrazinolysis. The neutral oligosaccharide fraction which comprised about 85% of the total sugar was fractionated into eight oligosaccharide fractions by Bio-Gel P-4 column chromatography. Occurrence of novel penta-antennary oligosaccharides in the larger three fractions was reported in the preceding paper (Yamashita, K., Kamerling, J.P., and Kobata, A. (1982) J. Biol. Chem. 257, 12809-12814). Structural studies of the remaining smaller oligosaccharides indicated that they all have Man alpha 1 leads to 6(Man alpha 1 leads to 3)Man beta 1 leads to 4GlcNAc beta 1 leads to 4GlcNAc as their common core. The alpha-mannosyl residues occur either free or as one of the following five groups: GlcNAc beta 1 leads to 2Man, GlcNAc beta 1 leads to 4Man, GlcNAc beta 1 leads to 4(GlcNAc beta 1 leads to 2)Man, GlcNAc beta 1 leads to 6(GlcNAc beta 1 leads to 2)Man, and GlcNAc beta 1 leads to 6(GlcNAc beta 1 leads to 4)(GlcNAc beta 1 leads to 2) Man. In most oligosaccharides, a beta-N-acetylglucosamine residue is linked at the C-4 position of the beta-mannosyl residue of the core. The structural characteristic of the sugar chains of hen ovomucoid indicated that they are not formed by the ordinary processing pathway of the asparagine-linked sugar chains.     

Requirements for the translocation of elongation-arrested, ribosome-associated OmpA across the plasma membrane of Escherichia coli

An oligodeoxynucleotide-dependent method to generate nascent polypeptide chains was adopted for use in a cell-free translation system prepared from Escherichia coli. In this way, NH2-terminal pOmpA fragments of distinct sizes were synthesized. Because most of these pOmpA fragments could be covalently linked to puromycin, precipitated with cetyltrimethylammonium bromide, and were enriched by sedimentation, they represent a population of elongation-arrested, ribosome-associated nascent chains. Translocation of these nascent pOmpA chains into inside-out membrane vesicles of E. coli required SecA and (depending on size) SecB. Whereas their translocation was strictly dependent on the H+-motive force of the vesicles, no indication for the involvement of the bacterial signal recognition particle was obtained. SecA and SecB, although required for translocation, did not mediate binding of the ribosome-associated pOmpA to membrane vesicles. However, SecA and SecB cotranslationally associated with nascent pOmpA, since they could be co-isolated with the ribosome-associated nascent chains and as such catalyzed translocation subsequent to the release of the ribosome. These results indicate that in E. coli, SecA also functionally interacts with preproteins before they are targeted to the translocase of the plasma membrane.     

Posttranscriptional aspects of the biosynthesis of type 1 collagen pro-alpha chains: the effects of posttranslational modifications on synthesis pauses during elongation of the pro alpha 1 (I) chain

Early studies indicated that chain elongation pauses were prominent during the in vivo synthesis of type I procollagen chains, and it was postulated [Kirk et al., (1987): J Biol Chem 262:5540-5545.] that these might have a role in the coordination of procollagen I molecular assembly. To examine this postulate, polysomes isolated from [(14)C]-Pro-labeled 3T6 cells were subjected to SDS-PAGE. The resulting gels were Western blotted and screened with a monoclonal antibody (SP1 .D8) directed against the N-terminal region of the pro alpha 1 (I) chain. The blots were fluorographed, which also permitted analysis of the pro alpha 2 (I) chain. There was a prominent pro alpha1 synthesis pause near the completion of full-length chain elongation, not matched by a pro alpha 2 pause. The amount of labeled polysome-associated near-full length pro alpha 1 (I) chains increased in parallel with labeling time. After 24 h in culture -[(14)C-Pro], collagen synthesis ceased but unlabeled polysome-associated pro alpha1 chains were readily detected by SP1 .D8. Change to fresh culture medium +[(14)C-Pro] reinitiated synthesis and permitted tracing of the newly synthesized labeled pro a chains through the polysome and intracellular compartments. The secreted procollagen molecules had a 2:1 pro alpha 1 (1):pro alpha 2 (I) chain ratio but the polysome-bound peptides did not. Pulse-chase experiments showed that near-full length pro alpha 1 (I) chains remained bound to polysomes as long as 4 h after reinitiation of translation but there was no evidence for pro alpha 2 (I) chain accumulation. The hydroxylation inhibitor alpha, alpha'-dipyridyl, and triple-helix inhibitors cis-hydroxyproline and 3,4 dehydroproline had minimal effects on the buildup of polysome-associated pro al chains. The glycosylation inhibitor tunicamycin also failed to change the final pro alpha 1 chain pausing, but it did cause the appearance of several discrete lower molecular weight pro alpha 1-related polypeptides that could not be accounted for simply as the result of lack of N-linked glycosylation in the C-propeptide regions. Disulfide bond experiments showed that some of the paused nascent polysome-associated pro alpha 1 (I) chains were disulfide bonded. Thus, while synthesis of pro alpha 1 (I) and pro alpha 2 (I) chains proceeds in parallel within the same ER compartments, their elongation rates are not coordinated. Interactions leading to heterotrimer formation are a late event which may affect the rate of release of the completed pro alpha 1 (I) chain from the polysome. The release of completed nascent pro alpha 1 (I) chains from their polysomal complexes is regulated by a mechanism not operating in the synthesis of pro alpha 2 (I) chains. The pro alpha 1 (I) chain release process is not connected directly with hydroxylation, glycosylation or triple-helix formation.     

Structure, function and gene expression of epithelial mucins

In this review the main characteristics, i.e., structure, function and gene expression, of the different mucins are discussed. Mucin-type molecules consist of a core protein moiety (apomucin) where a number of carbohydrate chains are attached to serines and threonines by glycosidic bonds. O-linked carbohydrates form up to 80% of the molecule and the length of the glucidic side chains varies from one to more than 20 residues. At least eight mucin-like genes have been isolated so far, and the main characteristic is the presence of a central domain composed of a variable number of "tandem repeats". The sequence homology of the central domain among the different members of the mucin-type family is limited, indicating that this internal domain is unique for each mucin. Thanks to the integrated results of genetic, immunological and biochemical studies, it is now possible to identify eight apomucin genes, namely MUC1, MUC2, MUC3, MUC4, MUC5AC, MUC5B, MUC6 and MUC7. MUC1 is the best characterized mucin and it is expressed on the apical surface of most polarized epithelial cells. The MUC1 gene has been cloned and sequenced. The MUC2 gene encodes a typical secretory gel-forming mucin which represents the predominant form in human intestinal and colon tissues. Another intestinal mucin is MUC3. The MUC4, MUC5AC and MUC5B genes have been isolated from a bronchial tissue cDNA library. The MUC4 and MUC5AC genes are mainly expressed in the respiratory tract, in gastric and reproductive mucosa, while MUC5B is highly detectable only in the bronchial glands. The MUC6 gene is expressed by gastric tissue and, recently, MUC7 has been cloned and sequenced using a salivary cDNA library.     

Surface enhanced Raman spectroscopy for characterization of structural characteristics of carbon chains in alpha1-acid glycoprotein and pseudoglycoproteins]

Surface-enhanced Raman scattering (SERS) spectroscopy was used to study the structure of carbohydrate chains in glycosylated forms of alpha 1-acid glycoprotein (AGP) and in pseudoglycoproteins obtained by transferring the carbohydrate chains of AGP to a polyacrylamide carrier. It was found that AGP-D glycoform and pseudoglycoproteins containing three or more glycans per molecule, which possess high immunomodulating activity, have a specific spatial organization of carbohydrate chains. This organization is maintained by the interaction of neighboring glycans with each other and does not depend on the nature of the carrier (whether it is polypeptide or polyacrylamide).     

The structure of the keratan sulphate chains attached to fibromodulin isolated from articular cartilage

Fibromodulin has been isolated from bovine and equine articular cartilage and the attached keratan sulphate chains subjected to digestion by keratanase II. The oligosaccharides generated have been reduced and subsequently isolated by strong anion-exchange chromatography. Their structures have been determined by high-field 1H-NMR spectroscopy and high-pH anion-exchange chromatography. Both alpha(2-6)- and alpha(2-3)-linked N-acetylneuraminic acid have been found in the capping oligosaccharides, and, fucose which is alpha(1-3)-linked to N-acetylglucosamine has been found as a branch in both repeat region and capping oligosaccharides. These data demonstrate that there are fundamental differences between the structures present in the N-linked keratan sulphate chains attached to fibromodulin from articular cartilage and those from tracheal cartilage, which lack both alpha(2-6)-linked N-acetylneuraminic acid and alpha(1-3)-linked fucose. It has been confirmed that the keratan sulphate chains are short, being only eight or nine disaccharides in length. Very significant differences in the levels of galactose sulphation have been identified at the non-reducing end of the chain. The galactose residue adjacent to the non-reducing cap is sulphated in only 1-3% of chains, compared with a sulphation level of over 40% closer to the reducing end. This highlights the difference between the chain termini and the repeat region in terms of structure and points to the potential for functional importance. The repeat region and capping fragments of the N-linked keratan sulphates from bovine and equine articular cartilage fibromodulin have been found to have the following general structure: NeuAc-(alpha 2-3/6)Gal[6SO3-](beta 1-4)GlcNAc6SO3-(beta 1-3)Gal[6SO3-] (beta 1-4)?[Fuc(alpha 1-3)]0-1GlcNAc6SO3-(beta 1-3)Gal-[6SO3-](beta 1-4)? 6-7GlcNAc6SO3-.     

Initiator RNA of discontinuous DNA synthesis in human lymphocytes

A short RNA covalently associated with nascent DNA has been isolated after synthesis in vitro with labeled ribonucleaside triphosphates and the removal of DNA by DNAase digestion. The RNA migrates in polyacrylamide gels or chromatographs on DEAE-Sephadex columns as a relatively discrete oligonucleotide 8-11 nucleotides in length. The RNA is associated primarily with nascent DNA with stoichiometry of approximately one per DNA chain. The RNA has a triphosphate group at the 5' end and 2 or 3 deoxynucleotide residues at the 3' end that are not removed by DNAase. These results further support a role for the RNA as an initiator of discontinuous DNA synthesis. Examination of sequences present at the 3' end of the RNA using RNAase to effect transfer of 32PO4 from 32P-labeled DNA to covalently attached RNA indicates that a diverse, rather than unique, set of sequences are present in the RNA.     

Carboxymethylation of thiol groups in ovalbumin: implications for proteins that contain both thiol and disulfide groups

The cysteine residues of hen ovalbumin were S-carboxymethylated with non-radioactive iodoacetic acid under various conditions by altering the pH at which the protein was denatured in 8 M urea, by using different molar ratios of non-radioactive iodoacetic acid to cysteine and by varying the time at which carboxymethylation was commenced after denaturing conditions had been applied. Under the various conditions, the thiol groups were carboxymethylated to different extents, the residual thiol groups being measured by reaction with 5,5'-dithiobis(2-nitrobenzoic acid) in the presence of sodium dodecyl sulfate. When ovalbumin is carboxymethylated in alkaline urea, it unfolds slowly and the carboxymethylation is incomplete even with 150-fold excess iodoacetic acid. The known rapid thiol-disulfide exchange that occurs at alkaline pH values makes this method of carboxymethylation unsuitable as a preliminary step for blocking the native cysteine residues of ovalbumin before reduction and labelling the thiol groups formed by reduction of the disulfide bonds. Titration of the thiol groups of ovalbumin in 6 M guanidine hydrochloride or 1% (w/v) sodium dodecyl sulfate at pH 8.2 with 5,5'-dithiobis(2-nitrobenzoic acid) is more rapid than in 8 M urea and these solvents would be preferable for studies of the disulfide-bonded sequences. Denaturation of ovalbumin in acidic 8 M urea is a very rapid process, and under mild acid conditions thiol-disulfide interchange is much slower. Subsequent carboxymethylation of the cysteine residues at alkaline pH with 150-fold excess iodoacetic acid results in complete carboxymethylation and the carboxymethylated ovalbumin can be reduced and labelled with radioactive iodoacetic acid with specific labelling of the half-cystine residues involved in the disulfide bond. The results are discussed in relation to the allocation of half-cystine residues in other protein systems that contain both thiol and disulfide groups.     

In vivo determination of replication origins of human mitochondrial DNA by ligation-mediated polymerase chain reaction

A large part of replication is aborted in human mitochondria, the result being a D-loop. As few attempts have been made to distinguish free 5' ends of true replicate from those of abortive ones, we examined the 5' ends of true replicate of human mitochondrial DNA at one nucleotide resolution in vivo by making use of ligation-mediated polymerase chain reaction. The distribution and relative amounts of origins of the true replicate are exactly the same as those of total newly synthesized heavy strands, which means that the abortion of replication is independent of 5' ends. Treatment of DNA with RNase H frees 5' ends on both heavy and light strands. This is the first in vivo evidence for covalently attached primer RNA to nascent strand in human mitochondrial DNA.