Sequencing of peptides phosphorylated on serines and threonines by post-source decay in matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

In the era of complete genome sequences, biochemical and medical research will focus more on the dynamic proteome of a cell. Regulation of proteins by post-translational modifications, which are not determined by the gene sequence, are already intensively studied. One example is phosphorylation of serines and threonines, probably the single most common cellular regulatory mechanism. In this paper we describe the sequencing of mono- and bisphosphorylated peptides, including identification of the phosphorylation sites, by post-source decay (PSD) in matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. In addition to dephosphorylation of the parent ions, we studied the influence of the phosphate group on the fragmentation of peptides. Generally, peptides phosphorylated on serine and threonine residues displayed no difference in their fragmentation patterns. The intensities of the resulting fragment ion signals depend only on the peptide sequence and not on either the phosphorylated amino acid or its position in the peptide chain. Phosphorylation increased the bond cleavage C-terminal to the phosphorylation site more than 10-fold, resulting in abundant signals, which typically dominated the PSD spectra. The produced C-terminally phosphorylated b-type fragment ions showed characteristic dephosphorylated fragment ions b(n) -H(3)PO(4) (-98 Da) and b(n) -HPO(3) (-80 Da) of higher abundances than the phosphorylated fragment ion. As a second layer to identify the phosphorylation site, all internally phosphorylated fragment ions were accompanied by minor, but always detectable, signals of the dephosphorylated fragment ions. Interpretation of PSD spectra of phosphopeptides was not more complicated than for unphosphorylated peptides, despite the increased number of obtained fragment ion signals.

Direct identification of major histocompatibility complex class I-bound tumor-associated peptide antigens of a renal carcinoma cell line by a novel mass spectrometric method

Melanoma and renal cell carcinoma (RCC) are thought to be the most immunogenic human tumors. Presently a series of tumor-specific peptides of melanoma is being tested in clinical trials with different immunotherapy protocols. In contrast, only one decameric peptide (SPSSNRIRNT) derived from one (ORF2) of three possible open reading frames (ORFs) of a gene named RAGE (Renal tumor AntiGEn) was shown to be the target for tumor-specific CTLs on renal carcinoma cells. One reason for the lack of identification of tumor antigens on RCC compared with melanoma may be the difficulty in generating tumor-specific CTLs as screening instruments. Therefore, our approach was directly to isolate and identify peptides bound to HLA class I molecules of the HLA-A2 and -B8 homozygous RCC line A-498. High performance liquid chromatography-fractionated peptides eluted with acid from immunoaffinity-purified HLA class I-peptide complexes were sequenced and identified for the first time by the novel and highly sensitive mass spectrometric method matrix-assisted laser desorption ionization-post source decay (MALDI-PSD) from minute amounts of 100 fmol to 1.5 pmol of the fractionated peptide samples. Fourteen peptide sequences first deduced from interpretations of the mass spectra were also shown to fulfill other reliability criteria such as matching the mass spectra of the respective synthetic peptides. Some peptides were identified to be derived from genes preferentially activated in malignant tissues or resulted from a possibly mutated gene. The most promising candidate for a CTL epitope is a decameric peptide (PASKKTDPQK) derived from another possible ORF (ORF5) of the RAGE gene and probably presented in association with HLA-B8. This peptide was synthesized and used for the in vitro induction of CTLs that lysed the A-498 cells and another HLA-B8-positive RCC line significantly more strongly than either other RAGE-positive but HLA-B8-negative RCC lines or K562 cells. Sensitive sequencing by MALDI-PSD thus may provide a powerful method of identifying potentially tumor-specific and HLA-restricted antigens, even on native malignant cells and tissues.

Structure determination of the small ubiquitin-related modifier SUMO-1

The recently discovered small ubiquitin-related modifier SUMO-1 belongs to the growing family of ubiquitin-related proteins involved in postranslational protein modification. Unlike ubiquitin, SUMO-1 does not appear to target proteins for degradation but seems to be involved in the modulation of protein-protein interactions. Independent studies demonstrate an essential function of SUMO-1 in the regulation of nucleo-cytoplasmic transport, and suggest a role in cell-cycle regulation and apoptosis. Here, we present the first three-dimensional structure of SUMO-1 solved by NMR. Although having only 18% amino acid sequence identity with ubiquitin, the overall structure closely resembles that of ubiquitin, featuring the betabetaalphabetabetaalphabeta fold of the ubiquitin protein family. In addition, the position of the two C-terminal Gly residues required for isopeptide bond formation is conserved between ubiquitin and SUMO-1. The most prominent feature of SUMO-1 is a long and highly flexible N terminus, which protrudes from the core of the protein and which is absent in ubiquitin. Furthermore, ubiquitin Lys48, required to generate ubiquitin polymers, is substituted in SUMO-1 by Gln69 at the same position, which provides an explanation of why SUMO-1 has not been observed to form polymers. Moreover, the hydrophobic core of SUMO-1 and ubiquitin is maintained by conserved hydrophobic residues, whereas the overall charge topology of SUMO-1 and ubiquitin differs significantly, suggesting specific modifying enzymes and target proteins for both proteins.

Extent and consequences of physician delay in the diagnosis of acral melanoma

The extent and consequences of professional delay in diagnosis were analysed in 83 patients with palmoplantar and subungual melanomas treated from January 1986 to March 1997 in our department. Seventeen (52%) out of 33 subungual melanomas and 10 (20%) out of 50 palmoplantar melanomas were clinically misdiagnosed by physicians. Three palmoplantar melanomas (6%) were initially misinterpreted by pathologists. In 23 of the 27 cases (85%) the clinical misdiagnosis was made by non-dermatologists. Misdiagnosis caused a median delay of 12 months in the diagnosis of palmoplantar melanomas and 18 months in the diagnosis of subungual melanomas. Delay in diagnosis was associated with increased tumour thickness, more advanced stage at time of melanoma diagnosis and a lower estimated 5-year survival rate (15.4% versus 68.9% for palmoplantar; 68.5% versus 90.9% for subungual). Acral melanomas are frequently misdiagnosed due to their less common locations and because plantar and subungual melanomas often do not fit the 'changing mole' pattern. To Improve the patient's prognosis it is necessary to increase the physicians' skill in the diagnosis of acral melanomas. Histological examination should always be performed in acral lesions that do not heal.

The change of therapy in esophagus carcinoma between 1975-1996

196 patients were assigned to an operation because of esophagus carcinoma between 20.05.1975 and 30.09.1996. Whereas until 1984 the surgical treatment was predominantly characterized by the uni-cavity operation, we increasingly practice the bi-cavity operation since them. By this procedure the resection rate could be extended up to 70.1%. As to be expected, most of the carcinomas were positioned in the medium third of the esophagus, the predominant tumor type was the squamos cell carcinoma, 85% of the patients had a stage three tumor. The mortality rate was 19.1% within the period of 6 weeks after the operation.

[Fluconazole-resistant Candida species from HIV infected patients with recurrent Candida stomatitis: cross resistance to itraconazole and ketoconazole]

In vitro susceptibility to fluconazole of Candida species isolated from 83 HIV-infected patients treated with fluconazole because of recurrent Candida stomatitis was monitored over a period of two years. A microdilution assay with high-resolution antifungal assay (HR) medium and RPMI 1640-medium were compared. In vitro less susceptible and fluconazole resistant C. species were observed in 23 patient at the end of the study. The Candida isolates recovered from oral rinsing fluids at the beginning and the end of study were tested for crossresistance to itraconazole and ketoconazole. Susceptibility to ketoconazole and to itraconazole was reduced using RPMI 1640-medium. Susceptibility of the isolates to fluconazole was not influenced by the assay medium. In 21 patients in vitro fluconazole resistant or less susceptible C. albicans were observed. 9 of 21 isolates showed crossresistance to itroconazole and ketoconazole, in 10 isolates only crossresistance to itraconazole was observed. During fluconazole treatment double infections due to combination of C. albicans and C. glabrata or C. krusei increased from 20% to 78% C. krusei was resistant to the three azoles. C. glabrata was less susceptible (4-8 mg/l) or resistant (> 8 mg/l) to fluconazole and resistant to itraconazole and ketoconazole High dosed intravenous fluconazole treatment with 400 to 600 mg daily failed in 11 patients with fluconazole resistant C. albicans and in 3 (3/10) patients with les susceptible C. albicans isolates.

Interleukin-6 secretion in mice is associated with reduced glucose-6-phosphatase and liver glycogen levels

Mice bearing interleukin-6 (IL-6)-secreting tumor were used to study the chronic effect of IL-6 on carbohydrate metabolism. Mice were injected with allogeneic tumor cells transduced with the murine IL-6 gene. Serum IL-6 levels were correlated exponentially with tumor weight. Secretion of IL-6 from the developed tumors was associated with decreased food consumption, reduced body weight, and reduced blood glucose levels. Insulin levels did not change, and 2-deoxyglucose uptake was not affected in most tissues examined. A significant increase of 2-deoxyglucose uptake was measured in the liver. Glycogen content in the liver determined 0, 6, 12, and 18 days after tumor inoculation was 42, 23, 12, and 3 mg/g, respectively. The activity of phosphoenolpyruvate carboxykinase was not affected. The activity of glucose-6-phosphatase (G-6-Phase) determined 6, 12, and 18 days after tumor injection was 84, 70, and 50% of G-6-Pase activity in pair-fed mice bearing nonsecreting tumors, respectively. G-6-Pase mRNA levels were markedly reduced due to inhibition of G-6-Pase gene transcriptional rate.

Tumor necrosis factor inhibits the transcriptional rate of glucose-6-phosphatase in vivo and in vitro

Recombinant human tumor necrosis factor-alpha (TNF) injection in mice was associated with a reduced blood glucose level, already manifest 6 hours following cytokine administration. Insulin levels were not affected. Glycogen content was decreased in a dose-dependent and time-response manner. The activity of glucose-6-phosphatase (G6Pase) was already reduced 6 hours after TNF injection and was sustained 12 hours afterward. Phosphoenolpyruvate carboxykinase (PEPCK) activity was not affected initially (6 hours after injection), but a 50% reduction was observed 12 hours following cytokine administration compared with levels in fasting controls. Both liver G6Pase and PEPCK mRNAs were markedly reduced due to an inhibition of the transcriptional rate. A direct inhibitory effect of TNF on G6Pase promoter activity was demonstrated using HuH-7 cells transiently transfected with G6Pase promoter, fused to a reporter gene.

Co-regulation of apo A-I, apo C-III and apo A-IV gene expression in human intestinal biopsies

The apo A-I gene is expressed in the liver and small intestine. In order to study the role of human intestinal transcription of the apo A-I gene in determining plasma high-density lipoprotein, (HDL)-cholesterol and apo lipoprotein (apo) A-I concentrations, the authors measured the relative mRNA levels of apo A-I in human intestinal biopsies. Biopsies were taken from 50 fasting subjects (25 males and 25 females). At the same time blood was taken for lipid and lipoprotein analysis. Plasma HDL-cholesterol correlated linearly with plasma apo A-I protein. No correlation could be demonstrated between intestinal apo A-I mRNA and plasma apo A-I or HDL-cholesterol levels. The apo A-I gene resides in an apolipoprotein cluster with the apo C-III and apo A-IV genes. To assess whether there is a coordinated expression of this locus, Northern blot analysis of intestinal RNA was performed. The authors have demonstrated that under fasting conditions mRNA levels of apo A-I, C-III and A-IV are co-regulated in the intestine.

Common genetic variation in the promoter of the human apo CIII gene abolishes regulation by insulin and may contribute to hypertriglyceridemia

Overexpression of plasma apolipoprotein CIII (apo CIII) causes hypertriglyceridemia in transgenic mice. A genetically variant form of the human apo CIII promoter, containing five single base pair changes, has been shown to be associated with severe hypertriglyceridemia in a patient population. In animals and in cultured cells the apo CIII gene is transcriptionally downregulated by insulin. In this study we demonstrate that, unlike the wild-type promoter, the variant promoter was defective in its response to insulin treatment, remaining constitutively active at all concentrations of insulin. The loss of insulin regulation was mapped to polymorphic sites at -482 and -455, which fall within a previously identified insulin response element. Loss of insulin regulation could result in overexpression of the apo CIII gene and contribute to the development of hypertriglyceridemia. The variant apo CIII promoter is common in the human population and may represent a major contributing factor to the development of hypertriglyceridemia.

Single-word auditory stimulation and regional cerebral blood flow as studied by SPECT

Single photon emission computed tomography (SPECT) examined changes in regional cerebral blood flow (rCBF) induced by passive auditory single-word stimulation. A split-dose SPECT technique was used between resting and activated states, in which a smaller amount of ligand (99m technetium hexamethyl propyleneamine oxide, HMPAO) was given with the first scan, accompanied by a prolonged scan time. A larger amount of ligand was given with the second scan, accompanied by a shorter scan time. This split-dose SPECT technique has met with previous success for other activation tasks. The brain regions of interest (ROIs) in this study were selected from ROIs previously found to be activated by passive auditory single-word stimulation and not by non-word stimuli in positron emission tomography (PET) rCBF studies. This study thus tested the sensitivity of SPECT with HMPAO to detect brain activation with a stimulus previously demonstrated to elicit changes in rCBF with PET. However, no significant difference was detected between resting and activated states in this study. Thus, SPECT was not as sensitive as PET in this activation task. Since SPECT is a less costly and more widely available modality to study brain activation than PET, it is important to delineate its potential capacities to maximize the efficiency of future research in this field.

Alternative polyadenylation of apolipoprotein B RNA is a major cause of B-48 protein formation in rat hepatoma cell lines transfected with human apoB-100 minigenes

The human apoB gene encodes an mRNA of 14121 nucleotides. In liver the apoB gene products a full-length mature protein of 4,536 amino acids (B-100), whereas in the intestine this gene produces a truncated protein of 2,152 amino acids (B-48). B-48 results from RNA editing of nucleotide 6666 from C to U, thereby producing a stop codon at position 2153. Rat liver has been shown to contain apoB RNA editing capability resulting in production of both B-100 and B-48. To create an in vitro expression system for human B-100, a minigene with a wild type coding sequence for the entire B-100 protein (B-100/Gln) was stably transfected into rat hepatoma cells (McA-RH7777). Similarly, a minigene with mutation at nucleotide 6667 that allowed translation even after editing of nucleotide 6666 (B-100/Leu, nonstop mutant), a minigene with an additional nonsense mutation at nucleotide 7053 to produce B-50 (B-50/Leu), and a truncated wild type minigene with a stop signal at codon 3261 to produce B-74 and an mRNA of 10 kb (B-74/Gln) were also transfected. Very little full-length B-100 and B-74 was produced by any of the respective constructions, including the B-100/Leu with the nonstop mutation. Transfection with B-100/Gln, B-100/Leu and B-74/Gln constructions produced greater than 90% of apoB as B-48, whereas the B-50/Leu construction produced 76% B-50 and 24% B-48. The inability of the B-100/Leu construction to produce B-100 suggested an explanation for B-48 production other than RNA editing. Northern blot analysis showed that the RNA produced by all four transfectants was shortened to a size of about 7 kb. A 10-kb but no 7-kb RNA was observed in the B-74/Leu construction when transfected to Chinese hamster ovary cells suggesting cell type specificity in generation of a shortened RNA. The 3' end of apoB RNA from McA-RH7777 B-100/Leu transfectants was reverse transcribed, cloned, and sequenced. This revealed two species of RNA: one polyadenylated at or near nucleotide 6775 capable of coding for B-48, the other polyadenylated at nucleotide 7080 capable of coding for B-50. In 18% of the cDNA clones, nucleotide 6666 was edited from C to T. In 6 of 34 clones, addition of the poly(A) tail after nucleotide 6774 created a TAA stop codon, whereas no stop signals could be detected in the remaining clones.(ABSTRACT TRUNCATED AT 400 WORDS)

Orphan receptor HNF-4 and bZip protein C/EBP alpha bind to overlapping regions of the apolipoprotein B gene promoter and synergistically activate transcription

As the sole protein component of low density lipoproteins, apolipoprotein B (apoB) plays an important role in cholesterol metabolism. Previously, we found that the proximal promoter region of apoB (-81 to -52 relative to the start site) played a critical role in hepatocyte-specific gene expression and that that region contained overlapping binding sites for nuclear factors AF-1 (-81 to -62) and C/EBP (-69 to -52) (Metzger, S., Leff, T., and Breslow, J. L. (1990) J. Biol. Chem. 265, 9978-9983). In this study, we show that HNF-4, a member of the steroid hormone receptor superfamily, binds the AF-1 site on the apoB promoter and through it activates transcription in transient transfection assays in both liver and non-liver cell lines, HepG2 and HeLa, respectively. Mutational analysis of the AF-1/HNF-4 binding site indicated a correlation of HNF-4 binding and transcriptional activity. In addition, transient co-transfection experiments with HNF-4 and C/EBP alpha expression vectors showed that the two factors can synergistically activate transcription to levels more than 3-fold above the sum of either factor alone. Finally, using gel retardation analysis we show that purified HNF-4 and C/EBP proteins can concurrently occupy their overlapping binding sites on the apoB promoter in vitro. However, since the same system showed a lack of cooperative binding, we argue that an alternative mechanism is responsible for the synergistic effect of HNF-4 and C/EBP alpha on apoB gene transcription.

Overexpression of the relA gene in Escherichia coli

Intracellular levels of guanosine 3',5'-bispyrophosphate (ppGpp) governed by the relA gene are normally regulated by aminoacyl-tRNA availability for protein synthesis. An experimental system is described in which cellular levels of ppGpp are controlled instead by induction of plasmid pKK223-3 derivatives with the relA structural gene, or portions thereof, under control of the Ptac promoter. In amino acid-rich media, isopropyl-1-thio-beta-D-galactopyranoside induction of transcription of the wild type relA gene in pSM10 yields about a 100-fold overexpression of a metabolically stable, full length (743 amino acid) RelA protein to levels approximating the number of cellular ribosomes. This overexpression is accompanied by a roughly parallel and relC-dependent elevation of ppGpp levels. Induction of a relA gene deletion mutant in pSM11 containing 455 amino-terminal amino acids results in much lower levels of expression of a metabolically unstable 55-kDa protein and elevated ppGpp levels that are almost equivalent to induced pSM10 and are relC-independent. Induction of a larger deletion in pSM12 containing 331 amino-terminal amino acids does not provoke ppGpp accumulation. We are able to elicit high levels of ppGpp without changing nutritional abundance and without massive overexpression of the RelA protein by inducing the metabolically unstable, truncated RelA protein. We find the effects of elevated ppGpp levels to include a slowing of growth, an inhibition of stable RNA accumulation, an inhibition of cellular rrn P1 promoter activities as measured by primer extension, and changes in the pattern of gene expression viewed by two-dimensional electrophoresis of cellular proteins.

Nuclear factors AF-1 and C/EBP bind to the human ApoB gene promoter and modulate its transcriptional activity in hepatic cells

ApoB-100, the major protein of low density lipoprotein, is produced primarily in the liver. The apoB promoter region from -86 to -52 binds two hepatic nuclear proteins. The protein that binds to the sequence between -86 to -61, called AF-1, was characterized and also shown to interact with the apoCIII, apoA-I, and apoCII promoters. We now show that the second protein, which by DNase I footprinting binds to the sequence between -69 and -52, is the heat stable hepatic factor C/EBP. The binding of this protein is competed by a known C/EBP-binding sequence in the transthyretin gene enhancer (TRR oligo 3). In addition, the protein protects the same region in DNase I footprinting as purified C/EBP. Mutants that affect AF-1 or C/EBP binding to the apoB promoter were created. These mutants were analyzed by the gel mobility shift assay and transient transfections into HepG2 cells. We have demonstrated that the two factors bind to overlapping sites and that they modulate apoB transcriptional activity.

Characterization of the relA1 mutation and a comparison of relA1 with new relA null alleles in Escherichia coli

The most widely studied "relaxed" mutant of the relA locus, the relA1 allele, is shown here to consist of an IS2 insertion between the 85th and 86th codons of the otherwise wild-type relA structural gene, which normally encodes a 743-amino acid (84 kDa) protein. The RelA protein is a ribosome-dependent ATP:GTP (GDP) pyrophosphoryltransferase that is activated during the stringent response to amino acid starvation and thereby occasions the accumulation of guanosine 3',5'-bispyrophosphate (ppGpp). We propose that the IS2 insertion functionally splits the RelA protein into two (alpha and beta) peptide fragments which can complement each other in trans to yield residual ppGpp synthetic activity; neither fragment shows this activity when expressed alone. Cell strains with a single copy relA null allele show physiological behavior that is much the same as relA1 mutant strains. Both relA1 and relA null strains accumulate ppGpp during glucose starvation and do not accumulate ppGpp during the stringent response. The presence of ppGpp in verifiable relA null strains is interpreted as unequivocal evidence for an alternate route of ppGpp synthesis that exists in addition to the relA-dependent reaction.

[Perioperative glucose resorption and hormonal reaction following intraduodenal glucose administration]

Early postoperative enteral nutrition has repeatedly been described in the literature but has not found its place yet in everyday clinical life. We conducted perioperative intraduodenal glucose tolerance tests in 12 patients with a healthy metabolism who had to undergo moderately severe abdominal surgery. Our results suggest that the resorption is still markedly delayed 12 h postoperatively and that the hormonal regulation is also essentially disturbed. Therefore, we believe that enteral nutrition in the early postoperative period is beneficial only more than 24 h after surgery.

Protein sequences encoded by the relA and the spoT genes of Escherichia coli are interrelated

relA and spoT are designations for two unlinked Escherichia coli genes whose products function in the synthesis and degradation of guanosine 3',5'-bispyrophosphate during the stringent regulatory response to amino acid deprivation. The RelA protein catalyzes an ATP:GTP 3'-pyrophosphoryl group transfer reaction, and the SpoT protein has a guanosine 3',5'-bispyrophosphate 3'-pyrophosphohydrolyase activity. Both genes have been sequenced recently; the relA gene produces an 84-kDa protein, and the spoT gene is deduced to encode a 79-kDa protein. We report here that the protein sequences of the relA and spoT genes are extensively interrelated.

Recombination and replication of plasmid-like derivatives of a short section of the mitochondrial chromosome of Neurospora crassa

The 21-kbp mitochondrial chromosome of the stp-ruv strain of Neurospora crassa undergoes regional amplification yielding plasmid-like supercoiled circles varying in size from subunit length to very high multimers. A comparison of the base sequence of the five plasmids studied, with the region of the chromosome from which they were derived, indicated that the amplified chromosomal segments were determined by a recombination-excision process near or within two structurally distinctive regions. One of these, consisting of nearly uninterrupted strings of Cs and Gs straddling tandem PstI site direct repeats, could form an extended hairpin loop with only a few mismatches. It was found at or near the 5' exchange point of all of the plasmids. An extended 35-bp sequence containing 17-bp direct repeats was the primary 3' site of exchange. Base sequence changes were found in the vicinity of exchange points. Most notable of these was a G insertion and T to C transition within a section of the 5' region likely to form a hairpin loop, suggesting the involvement of a mismatch repair-like mechanism in the recombination process. The sequence, TATATAGACATATA, was identified as a likely candidate for the site of replication initiation. A nearly identical sequence was found common to all of the corresponding plasmids of Podospora anserina and was reported near the presumed replication origin of the Drosophila yakuba mitochondrial chromosome. A search of GenBank revealed a remarkable association of the consensus sequence, TATATAGAXATATA, with the plus strand of organelle DNA.

Perioperative Glukoseresorption und hormonelle Reaktion nach intraduodenaler Glukoseapplikation

Eine frühpostoperative enterale Ernährung wird in der Literatur immer wieder beschrieben, hat sich aber im klinischen Alltag nicht durchsetzen können. An 12 stoffwechselgesunden Patienten, die sich mittleren abdominalchirurgischen Operationen unterziehen muβten, führten wir perioperative intraduodenale Glukosebelastungen durch. Durch unsere Ergebnisse können wir zeigen, daβ die Resorption nach 12 h postoperativ noch deutlich verzögert und auch die hormonelle Regulation erheblich gestört ist. Eine enterale Ernährung in der frühpostoperativen Phase erscheint uns deshalb erst nach mehr als 24 h sinnvoll.

The nucleotide sequence and characterization of the relA gene of Escherichia coli

The relA gene product of Escherichia coli is known to be responsible for the synthesis of guanosine 3',5'-bispyrophosphate (ppGpp) during the stringent response to amino acid starvation. This report presents the sequence of the relA gene region and assignment of its 743-codon open reading frame by the following criteria: 1) genetic complementation of ppGpp synthesis in a relaxed (relA1) mutant during the stringent response; 2) changes in 3-aminotriazole resistance during growth to mimic a relA+ phenotype; 3) verification of the presence of an amber codon at the normal carboxyl terminus of the relA gene; and 4) immunological assays of expression of the RelA protein. The apparent molecular mass of the cloned relA gene product is calculated to be 83,856 daltons and as visualized by immunoblotting is identical to that of the previously characterized protein. A promoter has been identified that directs relA gene transcription towards the pyrG gene, in a counterclockwise direction on the E. coli chromosome. Genomic Southern blot analyses verify that the relA regions cloned and subjected to nucleotide sequence analysis correspond to homologous regions on the E. coli chromosome.

Nucleotide sequence of the middle dsRNA segment of bacteriophage phi 6: placement of the genes of membrane-associated proteins

The genome of the lipid-containing bacteriophage phi 6 contains three segments of double-stranded RNA. We have determined the nucleotide sequence of cDNA derived from the middle-size RNA segment. The coding sequences of three proteins on this segment were identified on the basis of size and the correlation of predicted N-terminal amino acid sequences with those found through the analysis of isolated proteins. In contrast to our results with the small phi 6 dsRNA segment, the open reading frames are not tightly clustered. The homologous terminal noncoding regions between the middle and small dsRNA segments are found to be more extensive than RNA sequencing had previously indicated.

Serotyping and genotyping of encapsulated Escherichia coli K1 sepsis isolates with a monoclonal IgG anti K1 antibody and K1 gene probes

Among infectious diseases caused by E. coli the capsular type K1 plays a predominant role. E. coli K1 isolates account for 80% of cases of E. coli neonatal meningitis and 30% of E. coli sepsis strains. Serotyping of K1 strains has conventionally relied upon the use of K1-specific bacteriophages or serum agar methods with polyvalent anti K1 serum. In the study present here, 187 E. coli sepsis isolates have been analysed for production of the K1 antigen using K1 phages, K1 serum agar plates and Latex agglutination and ELISA using an IgG2a anti K1 monoclonal antibody. In total, 33 sepsis isolates (about 18%) were identified as K1 positive, with three of these strains proving negative in all tests except those exploiting the monoclonal antibody. That these three strains elaborate the K1 antigen was confirmed by Southern blot experiments using cloned K1 antigen production genes as probes. The failure of the three strains in all the tests except those that use monoclonal antibody could be explained by apparent disruption of K1 gene sequences that encode functions essential for the export of capsular material to the cell surface. The superiority of tests based on monoclonal antibodies above the conventional methods for detection of K1 antigen is evident.

Qualitative and quantitative determination of enterobacterial common antigen (ECA) with monoclonal antibodies: expression of ECA by two Actinobacillus species

The presence and quantity of the enterobacterial common antigen (ECA) in several species belonging to the family Enterobacteriaceae as well as to other gram-negative families were determined by a solid-phase enzyme-linked immunosorbent assay system and Western blotting by using mouse monoclonal antibodies specific for ECA. Except for Erwinia chrysanthemi, previously known to be an exception, all species known or presumed to belong to Enterobacteriaceae produced ECA (89 of 90 species). Most species not belonging to Enterobacteriaceae did not produce ECA (25 of 28 species), with one already known (Plesiomonas shigelloides) and two hitherto unknown (Actinobacillus equuli and Actinobacillus suis) exceptions. Interestingly, all strains of P. shigelloides produced ECA, regardless of the presence of the Shigella sonnei cross-reacting O antigen. Quantitation of the amount of ECA in members of the family Enterobacteriaceae revealed a remarkable heterogeneity among genera and species as well as within one species. We conclude that the rapid, sensitive, and reliable determination of ECA is a useful aid in taxonomic classification and may help to characterize the relatedness of the family Enterobacteriaceae to other families. However, a quantitative analysis of ECA appears to be without value for these purposes.

Impaired humoral immune response in complement C3-deficient guinea pigs: absence of secondary antibody response

A recently described genetically controlled C3 deficiency (C3D) in guinea pigs (GP) provided a unique model for studying the role of C3 in the afferent limb of the humoral immune response in a direct manner. These C3D animals, which have only 5-7% of normal serum C3 level, were immunized with the bacteriophage phi chi 174, a T cell-dependent antigen, followed by a booster injection after 4 weeks (1.5 X 10(9) plaque-forming units/kg). The formation of IgM and IgG antibody in the course of the primary and secondary response was determined and compared with a control group of inbred strain 2 GP. The C3D animals showed a markedly diminished antibody response to this antigen. Amplification of the antibody titer as well as regular isotype switching from IgM to IgG was absent in the secondary response. Increasing the amount of antigen to a high dose (1 X 10(10) plaque-forming units/kg) led to a normalization of the antibody response. The impairment in antibody formation resembles closely the impaired antibody response in C4-deficient or C2-deficient GP, which both have a block in activation of C3 via the classical pathway. However, in contrast to C4D GP or C2D GP the C3D GP do not exhibit serological characteristics of immune complex disease. They have normal levels of total serum IgM, of IgM anti-2,4-dinitrophenyl antibodies and of IgM rheumatoid factors.

The role and mechanism of cobra venom factor-induced suppression of the humoral immune response in guinea pigs

The cobra venom factor (CVF)-mediated suppression of the humoral immune response to bacteriophage phi X 174, a T cell-dependent antigen, was investigated in guinea pigs. The suppression was markedly dependent on the amount of antigen used: decomplementation of animals diminished the humoral immune response when immunizing with low doses of antigen, whereas increasing the antigenic dose resulted in little or no diminution by CVF. In contrast to the results with normal animals, CVF had no influence on the humoral immune response of genetically C2-deficient guinea pigs; i.e., no suppression occurred above that due to the inherited complement deficiency state alone. We therefore postulate that CVF suppresses the humoral immune response by the depletion of C3, with no measurable role for complement split products under these experimental conditions.

The role and mechanism of cobra venom factor-induced suppression of the humoral immune response in guinea pigs

The cobra venom factor (CVF)-mediated suppression of the humoral immune response to bacteriophage phi X 174, a T cell-dependent antigen, was investigated in guinea pigs. The suppression was markedly dependent on the amount of antigen used: decomplementation of animals diminished the humoral immune response when immunizing with low doses of antigen, whereas increasing the antigenic dose resulted in little or no diminution by CVF. In contrast to the results with normal animals, CVF had no influence on the humoral immune response of genetically C2-deficient guinea pigs; i.e., no suppression occurred above that due to the inherited complement deficiency state alone. We therefore postulate that CVF suppresses the humoral immune response by the depletion of C3, with no measurable role for complement split products under these experimental conditions.

Plasmodium falciparum: expression of the adenine phosphoribosyltransferase gene in mouse L cells

Genomic libraries of Plasmodium falciparum were constructed in the pBR322 plasmid. Using the DNA-mediated gene transfer technique, the genomic libraries were introduced into tissue-cultured mouse cells lacking the enzyme adenine phosphoribosyltransferase. Following selection for the adenine phosphoribosyltransferse phenotype, several colonies were isolated. All clones were shown to possess adenine phosphoribosyltransferase activity and pBR322 sequences. In addition, the Km value of adenine phosphoribosyltransferase (for adenine) from a transformant was found to be identical to that from P. falciparum. These results indicate that the adenine phosphoribosyltransferase gene of P. falciparum was successfully cloned and expressed in a mammalian system.

Detection of Plasmodium falciparum in blood using DNA hybridization

A rapid and simple assay for detecting Plasmodium falciparum in human blood was developed. The assay is based on DNA-DNA spot hybridization, using radiolabeled P. falciparum DNA as a probe and finger prick blood as the assay sample. It is very sensitive, able to detect parasitemia levels of 0.0001% in 10 microliter of blood. The assay can be quantified and used to estimate parasitemia levels. Several hundred blood samples can be processed simultaneously, and the entire procedure is completed within 24 hr. This assay can be useful for epidemiological surveys, for screening of blood by blood banks and for health authorities examining immigrants and tourists coming from malaria infested areas.

cDNA cloning of portions of the bacteriophage phi 6 genome

Phage phi 6 has a genome consisting of three pieces of double-stranded RNA. Single-stranded RNA was prepared from phi 6 nucleocapsids by in vitro transcription with the phage RNA polymerase. These transcripts were polyadenylated and used as templates for the preparation of cDNA copies. The resulting DNA was cloned into the PstI restriction nuclease site of plasmid pBR322. Insert-bearing plasmids were annealed to phi 6 RNA to assign the inserts to their proper segments. In this way we identified inserts corresponding to the large, medium, and small segments. Two large overlapping inserts of the small segment constitute the complete complement of the segment as determined by the sequence analysis of the DNA. In vitro coupled transcription and translation showed that the small segment inserts were able to direct the synthesis of the four known genes in the small segment. Two overlapping inserts in the medium segment constitute the entire segment and were shown to direct the in vitro synthesis of two of the three known proteins of the medium segment. Several inserts bearing about one-third the complement of the large segment were also isolated, and one of these directed the synthesis of a peptide that resembles protein P1. Restriction endonuclease maps were prepared for the inserts, and by in vitro synthesis it was possible to refine the genetic map of phi 6. A chimeric plasmid was constructed that combines plasmids pUC8 and RSF1010. Inserts placed on this plasmid were transformed to Pseudomonas phaseolicola, the natural host of phage phi 6. It was possible to refine further the genetic map by complementation of nonsense mutants of phi 6 with the cDNA.

Methylation pattern of mouse mitochondrial DNA

The pattern of methylation of mouse mitochondrial DNA (mtDNA) was studied using several techniques. By employing a sensitive analytical procedure it was possible to show that this DNA contains the modified base 5-methylcytosine (m5Cyt). This residue occurred exclusively at the dinucleotide sequence CpG at a frequency of 3 to 5%. The pattern of methylation was further investigated by determining the state of methylation of several MspI (HpaII) sites. Different sites were found to be methylated to a different extent, implying that methylation of mtDNA is nonrandom. Based on the known base composition and nucleotide sequence of mouse mtDNA, the dinucleotide sequence CpG was found to be underrepresented in this DNA. The features of mtDNA methylation (CpG methylation, partial methylation of specific sites and CpG underrepresentation) are also characteristic of vertebrate nuclear DNA. This resemblance may reflect functional relationship between the mitochondrial and nuclear genomes.