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D Perlman

Publications and source records attributed to D Perlman.

At least 37 records · Page 2Linked to original sources
PubMed1987

Improved resolution of DNA fragments in polysaccharide-supplemented agarose gels.

The electrophoretic separation of nucleic acids, including small DNA fragments in the range 50-1000 bp, is presently carried out in polyacrylamide gels or in gels containing high concentrations of agarose. We have developed an alternative gel matrix composition which is inexpensive, nontoxic, easy to prepare, and highly transparent to visible and uv light. The composition combines a soluble nonionic polysaccharide such as hydroxyethylcellulose, methylcellulose, or galactomannan with a minimum but sufficient concentration of agarose to form a gel which immobilizes the "liquid phase sieve." These mixtures do not replace polyacrylamide for resolving fragments smaller than approximately 75 nucleotides. However, the new gels show DNA fragment resolution (band separation versus distance traveled) and optical clarity superior to those of conventional agarose.

Carbohydrates↗
PubMed1987

Precise nucleotide sequence modifications with bidirectionally cleaving class-IIS excision linkers.

Bidirectionally cleaving blunt-ended DNA linkers have been constructed to generate defined nucleotide sequence modifications. The oligodeoxynucleotides (termed 'excision linkers'), contain two back-to-back recognition sites for class-IIS restriction endonucleases and provide a new instrument for modifying DNA primary structure. Following insertion of these linkers into host DNA, digestion with the cognate class-IIS enzyme results in a cleavage upstream and downstream from the adjoining enzyme recognition sites. Bidirectional cleavage efficiency can be improved by including spacer nucleotides between the two recognition sites. The number of nucleotides removed from or added to the host DNA depends upon the cleavage shift characteristic of the class-IIS enzyme, the design of the linker (including lateral spacer nucleotides to set the cleavage position), and the method used to make blunt ends from staggered ends following excision of the linker. BspMI linkers constructed in this study have been used to generate defined deletions in the ApR and TcR genes of pBR322. BsmI excision linkers are also described.

Base Sequence↗
PubMed1986

The MURFI linker for multiple reading frame insertion of a sense or nonsense codon into DNA.

Blunt-end palindromic DNA linkers with a central restriction site have been designed for the multiple reading frame insertion (abbreviated MURFI) of a sense or nonsense codon into DNA. We have utilized an amber MURFI linker, 5'CTAG TCTAGA CTAG3' to disrupt the lacZ gene, yielding truncated beta-galactosidase proteins. Conditional disruption of the tetr gene in E. coli has also been demonstrated. Nonsense codon MURFI linkers permit conditional fusion of multiple gene products while sense codon linkers can add structural elements (e.g. beta-turn, cationic segment, hydrophobic segment) or a desired amino acid to a protein (e.g. methionine, cysteine). Shotgun or alternatively site-directed insertion of the symmetric linkers is possible. The over-all length of the linker may be adjusted to retain the original reading frame, matching nucleotide additions or subtractions at recipient DNA sites. If a linker restriction site occurs elsewhere in the target DNA, single linker copies may still be inserted using non-phosphorylated linkers.

Base Sequence↗
PubMed1986

Mutations affecting the signal sequence alter synthesis and secretion of yeast invertase.

Insertion mutations previously constructed within the proximal region of the yeast invertase signal sequence did not interfere with secretion or glycosylation of the enzyme. We now describe deletion mutations within the same signal sequence. Large deletions truncating the hydrophobic core of the signal peptide prevented both secretion and glycosylation of the enzyme and increased the intracellular concentration of nonglycosylated invertase. This increase was coupled with the appearance of a new invertase polypeptide, 2 kilodaltons larger than cytoplasmic invertase. The new polypeptide was consistent in size with uncleaved (signal peptide intact) pre-secretory invertase previously identified by using in vitro translation (apparent molecular mass, 62 kilodaltons). The data on enzyme activity indicate that invertase whose secretion is aborted by large deletion mutations augments the normal pool of cytoplasmic invertase found in sucrose-fermenting yeast cells.

Base Sequence↗
PubMed1985

Blood flow in the arm under brachial plexus anaesthesia.

Changes in blood blow and skin temperature have been measured in the arms of twenty patients under brachial plexus anaesthesia. A rise in each was noted in every patient. The patients were subdivided into two groups of ten. The anaesthetic administered to the patients of one group contained adrenaline (1 in 100,000), and the patients in the other group received the same anaesthetic but with no added adrenaline. The rise in flow volume, flow velocity and temperature was greater in the group which received adrenaline. The difference in change of flow volume was significant (P less than 0.05), the difference in temperature rise highly significant (P less than 0.01), but the difference in change of flow velocity was not significant.

Adolescent↗
PubMed1984

Conformational alterations in the proximal portion of the yeast invertase signal peptide do not block secretion.

Various amino acid insertions have been introduced into the proximal portion of the signal sequence of secreted yeast invertase. The altered invertase genes have been reintroduced into yeast and monitored for their ability to direct synthesis of secreted invertase in vivo. The insertions should alter the signal polypeptide local secondary structure as predicted by the Chou and Fasman rules (1978). Secretion of these altered invertase polypeptides is not blocked by the amino acid insertions.

Biological Transport↗
PubMed1984

Cytoplasmic and secreted Saccharomyces cerevisiae invertase mRNAs encoded by one gene can be differentially or coordinately regulated.

A single structural gene, SUC2, encodes both secreted and cytoplasmic invertase in Saccharomyces cerevisiae. It is known that the unprocessed polypeptides which differ by a secretion signal sequence are encoded by separate mRNAs. This unusual transcriptional organization raises the question as to the degree to which the transcripts can be independently regulated. To define a system for studying this problem, we examined invertase transcription after various physiological perturbations of cells: rapid catabolite derepression, heat shock, and cell cycle arrest. With each treatment, fluctuations in mRNA levels for both cytoplasmic and secreted invertase were observed. We concluded that (i) catabolite-derepressed synthesis of the mRNAs occurs rapidly after a drop in glucose, is a sustained response, and does not require de novo protein synthesis; (ii) heat shock transcription of both invertase mRNAs is, in contrast, a brief and transient response requiring de novo protein synthesis; and (iii) alpha-mating hormone treatment (G1 phase arrest and release) results in regular and coordinated synthesis of both mRNAs midway between rounds of histone mRNA synthesis. We propose that invertase mRNA regulation involves constitutively synthesized transcriptional factors (observed during catabolite derepression) and transient factors (observed during heat shock and possibly during synchronous growth). Moreover, the mRNA levels for secreted and cytoplasmic invertase can be independently regulated.

Cell Cycle↗
PubMed1983

A putative signal peptidase recognition site and sequence in eukaryotic and prokaryotic signal peptides.

Presecretory signal peptides of 39 proteins from diverse prokaryotic and eukaryotic sources have been compared. Although varying in length and amino acid composition, the labile peptides share a hydrophobic core of approximately 12 amino acids. A positively charged residue (Lys or Arg) usually precedes the hydrophobic core. Core termination is defined by the occurrence of a charged residue, a sequence of residues which may induce a beta-turn in a polypeptide, or an interruption in potential alpha-helix or beta-extended strand structure. The hydrophobic cores contain, by weight average, 37% Leu: 15% Ala: 10% Val: 10% Phe: 7% Ile plus 21% other hydrophobic amino acids arranged in a non-random sequence. Following the hydrophobic cores (aligned by their last residue) a highly non-random and localized distribution of Ala is apparent within the initial eight positions following the core: (formula; see text) Coincident with this observation, Ala-X-Ala is the most frequent sequence preceding signal peptidase cleavage. We propose the existence of a signal peptidase recognition sequence A-X-B with the preferred cleavage site located after the sixth amino acid following the core sequence. Twenty-two of the above 27 underlined Ala residues would participate as A or B in peptidase cleavage. Position A includes the larger aliphatic amino acids, Leu, Val and Ile, as well as the residues already found at B (principally Ala, Gly and Ser). Since a preferred cleavage site can be discerned from carboxyl and not amino terminal alignment of the hydrophobic cores it is proposed that the carboxyl ends are oriented inward toward the lumen of the endoplasmic reticulum where cleavage is thought to occur. This orientation coupled with the predicted beta-turn typically found between the core and the cleavage site implies reverse hairpin insertion of the signal sequence. The structural features which we describe should help identify signal peptides and cleavage sites in presumptive amino acid sequences derived from DNA sequences.

Amino Acid Sequence↗
PubMed1982

Presecretory and cytoplasmic invertase polypeptides encoded by distinct mRNAs derived from the same structural gene differ by a signal sequence.

Saccharomyces cerevisiae strain FH4C carries a single invertase structural gene, SUC2, but produces distinct invertase mRNAs and polypeptides for the secreted and cytoplasmic forms of the enzyme. The two major invertase cell-free translation products are polypeptides of 60,000 daltons (p60) and 62,000 daltons (p62) and correspond to the nonglycosylated cytoplasmic form of invertase and the precursor of glycosylated secreted invertase, respectively. This paper describes amino acid sequence and peptide map analyses of invertase polypeptides. The peptide maps demonstrate that p62, p60, and the in vivo secreted polypeptide have significant structural homology. Sequence analysis, however, revealed differences between p62 and p60 at their amino termini. p62 contains an amino-terminal signal sequence of 19 amino acid residues that is specifically cleaved during secretion in a cell-free system to generate the secreted 87,000-dalton invertase glycopeptide gp87. This signal sequence is not present in p60. p60 synthesis begins with a methionine which can be aligned with a methionine at residue 21 in p 62. During translation, the p60 initiator methionine is removed and the newly generated amino terminus is acetylated. Based on peptide map similarities, partial amino-terminal sequence data, and common genetic origin, it is suggested that p60 and p62 have identical amino acid sequences carboxy-terminal to the p60 initiator methionine (residue 21 of p62). The reciprocal correlations of signal sequence with secretion and absence of signal sequence with cytoplasmic localization provide proof of the signal hypothesis for secreted proteins. Two mechanisms are proposed for the derivation of p60 and p62 from a single structural gene: alternative promoter sites, and differential processing of a single primary transcript.

Amino Acid Sequence↗
PubMed1981

Distinct repressible mRNAs for cytoplasmic and secreted yeast invertase are encoded by a single gene.

We have studied regulation of invertase putative structural genes (SUC) in S. cerevisiae and the synthetic relationship between secreted, glycosylated invertase (E.C.3.2.1.26) and the cytoplasmic, nonglycosylated form of the enzyme. Using immunoprecipitation and gel electrophoresis, we have analyzed invertase polypeptides and glycopeptides synthesized in vitro and in vivo. Analysis of size-fractionated mRNA from a SUC2 strain has shown that three mature, catabolite-repressible mRNA species direct the in vitro synthesis of three invertase polypeptides that have differing molecular weights. Two of these polypeptides, P63 and P62 (63 and 62 kd), are larger than the polypeptides of the secreted enzyme and are cotranslationally processed by microsomal membranes in vitro to yield secreted invertase glycopeptides (GP90 and GP87). The smallest polypeptide, P60 (60 kd), which comigrates electrophoretically with cytoplasmic invertase, is not processed. Posttranslationally, a microsomal-membrane detergent extract removes approximately 20 aminoacids from P62 but not from P60. In vitro translations of mRNAs from a genetically confirmed suc3 mutant strain, from the parental SUC3 strain and from derivative meiotic segregants have shown that the three polypeptides (and therefore three mRNA species) are encoded by one gene. Analysis of in vivo radiolabeled invertase from the same SUC3 and suc3 strains has verified that the SUC3 locus contains the structural gene for secreted and cytoplasmic invertase. Through the derepressed synthesis of multiple primary or processed transcripts, the SUC2 and SUC3 genes are regulated to produce multiple invertase polypeptides. The larger two polypeptides appear to be processed and secreted to yield glycosylated invertase, while the smallest remains in the cytoplasm.

Cytoplasm↗
PubMed1981

Microbial production of vitamin B12 antimetabolites. IV. Isolation and identification of 4-keto-5-amino-6-hydroxyhexanoic acid.

4-Keto-5-amino-6-hydroxyhexanoic acid was isolated from Bacillus cereus 102804 fermentations and found to inhibit the growth of Gram-positive and Gram-negative bacteria, when grown in a chemically defined medium. The mechanism appeared to be the inhibition of delta-aminolevulinic acid dehydratase. The Ki value of 4-keto-5-amino-6-hydroxyhexanoic acid in an enzyme preparation of Propionibacterium shermanii was 0.72 microM. Similar test conditions with 4-keto-5-aminohexanoic acid resulted in Ki of 12.1 microM. In both cases competitive inhibition was found. The structure of 4-keto-5-amino-6-hydroxyhexanoic acid was determined.

Aminocaproates↗