Biomedical subjects
Publications and source records attributed to D F Hill.
A program is described for sequence data entry which allows flexible program control by responding to both the keyboard and a sonic digitizer concurrently. Simplification of the initialization stage of each gel reading has been achieved, in comparison with other programs.
A second autonomous replicon of P307, RepFIB, has been isolated that has significant homology with other replicons in IncFI group plasmids. Eleven homologous repeats of 21 base pairs are present on the sequence and flank an open reading frame capable of coding for a protein of about Mr = 40,000. This protein was identified by maxicell analysis of cloned RepFIB. A series of deletion mutations of RepFIB were inserted into a DNA polymerase I-dependent vector and examined for their replication proficiency in a polA1 strain. These experiments defined a minimal replication region of 1.6 kilobases which includes the three repeats immediately upstream and downstream of the open reading frame. Deletion of a second set of repeats further downstream doubled the copy number of a chimeric plasmid replicating under RepFIB control. It was concluded that these repeats control the copy number of the replicon. Incompatibility tests showed that all three sets of repeats could express incompatibility with a resident RepFIB plasmid.
Examination of the nucleotides following the ATG or GTG initiation codons of a file of 251 genes from Escherichia coli has shown that 247 (98.4%) of them contain a sequence of at least three and 168 (66.9%) of them a sequence of at least four consecutive nucleotides that is complementary to some part of the 16 nt at the 5' terminus of the bacterial 16S rRNA. It is proposed that this sequence, which falls within the first 24 nt coding for the genetic message, might be involved in mRNA recognition through a mechanism analogous to the well-established 'Shine--Dalgarno' interaction with the 3' terminus of the 16S rRNA. Comparison of these data with data derived from a file of 117 'false' gene starts that have a Shine--Dalgarno-like sequence followed by a suitably spaced ATG or GTG triplet but which are believed not to lie at the beginnings of genetic messages shows the association that we have found to be statistically significant at the 99.9% level.
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We report a family with the X-linked eye disorder Norrie's disease, in which DNA analysis enabled the distinction to be made between female carriers and non carriers. There was perfect cosegregation of the disease gene and the restriction fragment length polymorphism DXS7 which is recognised by the probe L1.28. Adding our data to those already on record, the lod score for linkage between DXS7 and Norrie's disease reaches 5.6, for a recombination fraction of 0.0. We anticipate that DNA testing will become a major investigative tool in genetic counselling.
RepFIC is a basic replicon of IncFI plasmid P307 which is located within a 3.09-kilobase SmaI fragment. The nucleotide sequence of this region has been determined and shown to be homologous with the RepFIIA replicon of IncFII plasmids. The two replicons share three homologous regions, HRI, HRII, and HRIII, which are flanked by two nonhomologous regions, NHRI and NHRII. A comparison of coding regions reveals that the two replicons have several features in common. RepFIC, like RepFIIA, codes for a repA2 protein with its amino-terminal codons in HRI and its carboxy-terminal codons in NHRI. Although the codons for the repA1 proteins are located in NHRII, the DNA region containing a putative promoter, ribosomal binding site, and initiation codons is located in HRII. This region also codes for an inc RNA. There are nine base-pair differences between the inc RNA of RepFIIA and that of RepFIC, and as a result, RepFIC and RepFIIA replicons are compatible. An EcoRI fragment from the F plasmid which shows homology with RepFIC of P307 has also been sequenced. This fragment contains only a portion of RepFIC, including the genes for the putative repA2 protein and inc RNA. The region coding for a putative repA1 protein is interrupted by the transposon Tn1000 and shows no homology with the repA1 region of RepFIIA and RepFIC of P307. Our comparative and structural analyses suggest that RepFIC and RepFIIA, although different, have a similar replication mechanism and thus can be assigned to the same replicon family, which we designate the RepFIIA family.
Lysosomal degradation of the carbohydrate portion of glycoproteins and glycosaminoglycans produces monosaccharides and sulphate, which must efflux from the lysosomes before re-entering biosynthetic pathways. We examined the degradation of glycoproteins and glycosaminoglycans by lysosomes isolated from cultured human diploid fibroblasts. Cells were grown for 24 h in medium containing [3H]glucosamine and [35S]sulphate. When lysosomes are isolated from these cells, they contain label primarily in macromolecules (glycoproteins and glycosaminoglycans). Glycoprotein degradation by isolated lysosomes was followed by measuring the release of tritiated sugars from macromolecules and efflux of these sugars from the organelles. Glycosaminoglycan degradation was monitored by the release of both tritiated sugars and [35S]sulphate. During macromolecule degradation, the total amounts of free [35S]sulphate, N-acetyl[3H]glucosamine and N-acetyl[3H]galactosamine found outside the lysosome parallels the amounts of these products released by degradation. The total degradation of glycoproteins and glycosaminoglycans by intact cultured cells was also examined. The lysosomal contribution to degradation was assessed by measuring inhibition by the lysosomotropic amine NH4Cl. After 48 h incubation, inhibition by NH4Cl exceeded 55% of glycoprotein and 72% of glycosaminoglycan degradation. Recycling of [3H]hexosamines and [35S]sulphate by intact cells was estimated by measuring the appearance of 'newly synthesized' radioactively labelled macromolecules in the medium. Sulphate does not appear to be appreciably recycled. N-Acetylglucosamine and N-acetylgalactosamine, on the other hand, are reutilized to a significant extent.
Oligonucleotide-directed mutagenesis of cloned Rhodospirillum rubrum ribulose bisphosphate carboxylase/oxygenase with a synthetic 13mer oligonucleotide primer was used to effect a change at Met-330 to Leu-330. The resultant enzyme was kinetically examined in some detail and the following changes were found. The Km(CO2) increased from 0.16 to 2.35 mM, the Km(ribulose bisphosphate) increased from 0.05 to 1.40 mM for the carboxylase reaction and by a similar amount for the oxygenase reaction. The Ki(O2) increased from 0.17 to 6.00 mM, but the ratio of carboxylase activity to oxygenase activity was scarcely affected by the change in amino acid. The binding of the transition state analogue 2-carboxyribitol 1,5-bisphosphate was reversible in the mutant and essentially irreversible in the wild type enzyme. Inhibition by fructose bisphosphate, competitive with ribulose bisphosphate, was slightly increased in the mutant enzyme. These data suggest that the change of the residue from methionine to leucine decreases the stability of the enediol reaction intermediate.
Rat liver clathrin coated vesicles (CVs) were separated into several distinct subpopulations using non-sieving concentrations of agarose, which allowed the separation of species differing primarily in surface charge. Using preparative agarose electrophoresis (Kedersha, N. L., and L. H. Rome, 1986, Anal. Biochem., in press), the CVs were recovered and analyzed for differences in morphology, coat protein composition, and stripped vesicle protein composition. Coat proteins from different populations appeared identical on SDS PAGE, and triskelions stripped from the different populations showed the same mobility on the agarose gel, suggesting that the mobility differences observed in intact CVs were due to differences in the surface charge of underlying vesicles rather than to variations in their clathrin coats. Several non-coat polypeptides appeared to segregate exclusively with different populations as resolved by two-dimensional electrophoresis. Stripped CVs also exhibited considerable heterogeneity when analyzed by Western blotting: the fast-migrating population was enriched in the mannose 6-phosphate receptor, secretory acetylcholine esterase, and an Mr 195,000 glycoprotein. The slow-migrating population of CVs was enriched in the asialoglycoprotein receptor, and it appeared to contain all detectable concanavalin A-binding polypeptides as well as the bulk of detectable WGA-binding proteins. When CVs were prepared from 125I-asialoorosomucoid-perfused rat liver, ligand was found in the slow-migrating CVs, suggesting that these were endocytic in origin. Morphological differences were also observed: the fast-migrating population was enriched in smaller CVs, whereas the slow-migrating population exhibited an enrichment in larger CVs. As liver consists largely of hepatocytes, these subpopulations appear to originate from the same cell type and probably represent CVs of different intracellular origin and destination.
Highly purified cultures of rat astrocytes and oligodendrocytes were examined for their ability to bind and internalize lysosomal enzymes. Astrocytes displayed a saturable uptake of beta-glucosidase and beta-galactosidase. The uptake was specifically inhibited by mannose-6-phosphate but not by several other sugars or sugar phosphates, indicating that the process was mediated by mannose-6-phosphate receptors. When cells were allowed to take up 125I-beta-glucosidase for 1 hr at 37 degrees C and subcellular organelles were isolated, the enzyme was shown to comigrate with a lysosomal organelle marker enzyme, suggesting that the enzyme was targeted to lysosomes. Astrocyte receptors were probed directly by binding of 125I labeled beta-glucosidase to astrocyte membranes at 4 degrees C. Binding was saturable and competitively inhibited by mannose-6-phosphate. In contrast to the astrocytes, cultured oligodendrocytes showed no specific binding or uptake of the lysosomal enzymes. Immunocytochemical staining of mixed glial cultures supported the biochemical data; only the astrocytes stained positive with anti-mannose-6-phosphate receptor antibodies.
Acetyl coenzyme A has been shown to be required for heparan sulfate degradation for the acetylation of terminal alpha-linked glucosamine residues (Klein, U., Kresse, H., and von Figura, K. (1978) Proc. Natl. Acad. Sci. U.S.A. 75, 5185-5189). We can now demonstrate this requirement in intact isolated lysosomes. When lysosomes deficient in the enzyme alpha-N-acetylglucosaminidase were incubated at 37 degrees C with [3H]acetyl-CoA, tritium was incorporated primarily into glycosaminoglycans. By utilizing hydrolytic enzymes of known specificity, the labeled glycosaminoglycan was identified as heparan sulfate and the radioactivity was shown to be located in acetyl moieties of terminal alpha-N-acetylglucosamine residues. The acetylation of heparan sulfate in alpha-N-acetylglucosaminidase-deficient lysosomes could be stimulated by the addition of 0.5 mM ATP. Lysosomes from normal cells produced some labeled heparan sulfate; however, these organelles showed a significant incorporation of [3H]acetate into free N-acetylglucosamine that was increased over 10-fold by the addition of ATP. The N-acetylation was catalyzed by the enzyme acetyl-CoA:alpha-glucosaminide N-acetyltransferase since lysosomes deficient in this enzyme were unable to incorporate [3H]acetate into either heparan sulfate or N-acetylglucosamine even in the presence of ATP. Incorporation of [3H]acetate from [3H]acetyl-CoA into heparan sulfate (by alpha-N-acetylglucosaminidase-deficient lysosomes) and into N-acetylglucosamine (by normal lysosomes) showed a similar concentration dependence. The concentration for half-maximal incorporation of [3H]acetate was approximately 1 microM for both.
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The amino-acid sequence of the single-stranded DNA-binding protein of bacteriophage Pf1 and the nucleotide sequence of the corresponding gene have been determined. The protein has 144 amino acids and a molecular weight of 15 400; the gene consists of 435 nucleotides. The amino-acid sequence was determined by Edman degradation, carboxypeptidase A, B, and P digestion of intact protein and of peptides derived by chymotrypsin, Staphylococcus aureus V8 protease, and trypsin digestion. The nucleotide sequence was determined by the dideoxy method after random cloning of fragments of Pf1 DNA into M13. No sequence homology could be established between the amino-acid sequence of the DNA-binding protein of Pseudomonas aeruginosa-specific bacteriophage Pf1 and bacteriophage fd of Escherichia coli.
The nucleotide sequence of the DNA of the filamentous coliphage f1 has been determined. In agreement with earlier conclusions, the genome was found to comprise 6,407 nucleotides, 1 less than that of the related phage fd. Phage f1 DNA differs from that of phage M13 by 52 nucleotide changes, which lead to 5 amino acid substitutions in the corresponding proteins of the two phages, and from phage fd DNA by 186 nucleotide changes (including the single-nucleotide deletion), which lead to 12 amino acid differences between the proteins of phages f1 and fd. More than one-half of the nucleotide changes in each case are found in the sequence of 1,786 nucleotides comprising gene IV and the major intergenic region between gene IV and gene II. The sequence of this intergenic region (nucleotides 5501 to 6005) of phage f1 differs from the sequence reported by others through the inclusion of additional single nucleotides in eight positions and of a run of 13 nucleotides between positions 5885 and 5897, a point of uncertainty in the earlier published sequence. The differences between the sequence of bacteriophage f1 DNA now presented and a complete sequence for the DNA previously published by others are discussed, and the f1 DNA sequence is compared with those of bacteriophages M13 and fd.
The report of endorphin-like activity in human CSF [7] has stimulated us to study peptides in various CSF specimens. At first we attempted to fractionate CSF by gel-filtration and paper-mapping procedures. By these techniques, we have isolated a peptide (Gly-Ala3-Val-Leu) contaminated with glutamic acid (or glutamine), which could not be removed by either of these methods. An HPLC method was developed for peptide fractionations on a RP-18 column with a gradient of 18 mM ammonium acetate and acetonitrile. This system has been evaluated with synthetic peptides of molecular weight up to about 1850, and has the advantages that the buffer salts may be removed by lyophilization and separations are performed at or near neutral pH thus minimizing alterations in the structure of the peptides. The retention characteristics of peptides on a C18 column is a function of the pH of the buffer. This facilitates the characterization of peptides since each may be identified by its unique chromatographic behavior at different pH values on one column.
The sequence of nucleotides comprising genes V, VII, and VIII of bacteriophage f1 was determined. The sequence was found to differ from that of the corresponding region of the related fd genome by eight base substitutions in gene V and one in gene VIII. The structure of gene VII was completely conserved between these two viruses and was identical to that of bacteriophage M13. Both transitions and transversions were found in cases where bases were substituted, but all substitutions were in the third codon position and had no effect on the structure of the corresponding protein product. The gene V protein product could thus be deduced to be identical to that of the corresponding proteins from bacteriophages fd and M13. A potential EcoRII cleavage site was formed by nucleotides 172 to 176 of gene V. Replicative form DNA form DNA from bacteriophage f1 is normally resistant to this enzyme, and evidence is presented to suggest that the sequence was modified through methylation of cytosine 173. The probable locations of other modified nucleotides in the sequence are discussed.
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