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PubMed1997

In vivo observation of polypeptide flux through the bacterial chaperonin system.

The quantitative contribution of chaperonin GroEL to protein folding in E. coli was analyzed. A diverse set of newly synthesized polypeptides, predominantly between 10-55 kDa, interacts with GroEL, accounting for 10%-15% of all cytoplasmic protein under normal growth conditions, and for 30% or more upon exposure to heat stress. Most proteins leave GroEL rapidly within 10-30 s. We distinguish three classes of substrate proteins: (I) proteins with a chaperonin-independent folding pathway; (II) proteins, more than 50% of total, with an intermediate chaperonin dependence for which normally only a small fraction transits GroEL; and (III) a set of highly chaperonin-dependent proteins, many of which dissociate slowly from GroEL and probably require sequestration of aggregation-sensitive intermediates within the GroEL cavity for successful folding.

Bacterial Proteins↗
PubMed1999

Structural properties of Friedreich's ataxia d(GAA) repeats.

The expansion of trinucleotide repeat sequences is the underlying cause of a growing number of inherited human disorders. To provide correlations between DNA structure and mechanisms of trinucleotide repeat expansion, we investigated potential secondary structures formed from the complementary strands of d(GAA.TTC)n, a sequence whose expansion is associated with Friedreich's ataxia. In 50 mM NaCl, pH 7.5, d(GAA)15 exhibited a cooperative and reversible decrease in large circular dichroism bands at 248 and 272-274 nm over the temperature range of 5-50 degrees C, providing evidence for a base-paired structure at reduced temperatures. Ultraviolet absorbance melting profiles indicated that the melting temperature (Tm) of d(GAA)15 was 40 degrees C. At 5 degrees C, the central portion of d(GAA)15 was hypersensitive to single-strand-specific P1 nuclease degradation and diethyl pyrocarbonate modification, providing evidence for a hairpin conformation. At temperatures between 25 and 35 degrees C in 50 mM NaCl, the triplet repeat region of d(GAA)15 was uniformly resistant to degradation by P1 nuclease, including the central portion of the sequence. Our results indicate that the structure of d(GAA)15 is a hairpin at 5 degrees C, unknown but partially base-paired at 37 degrees C, and an approximately random coil above 65 degrees C.

Circular Dichroism↗
PubMedDate not supplied

Synthesis and in vitro evaluation of glutamide-containing cationic lipids for gene delivery.

A novel series of cationic amphiphiles based on dialkyl glutamides with cationic pyridinium head group were synthesized as potential gene delivery agents. Four cationic lipids with glutamide as linker and varying chain lengths were tested for their transfection efficiency in three cell lines. The DNA-lipid complexes were characterized for their ability to bind to DNA, protection from nuclease digestion, size, zeta-potential, and toxicity. All four lipids demonstrated efficient transfection in MCF-7, COS, and HeLa cells, and the reporter gene expression was much higher with DOPE as the helper lipid in the formulation when compared to cholesterol. Among these 14-carbon lipids, lipid 2 has shown the highest transfection efficiency, complete protection of DNA from nuclease digestion, and low toxicity. Interestingly, lipid 2 has also shown remarkable enhancement in transfection in the presence of serum.

Animals↗
PubMed1993

Isotope effects on the cleavage of DNA by bleomycin: mechanism and modulation.

Sequence-specific isotope effects on the cleavage of DNA at thymidine residues by activated iron.bleomycin (Fe.BLM) have been observed upon incorporation of [4'-2H]thymidine into the DNA. The effects may be quantitated by end-labeling the DNA with phosphorus-32, generating a sequence ladder by gel electrophoresis, and measuring the relative damage at cleavage sites by autoradiography or phosphorimager technology. Results with DNA deuteriated at other positions of the deoxyribose ring, such as, the 5'- or 2'-carbon, afford no isotope effect suggesting high regiospecificity for the BLM-mediated carbon-hydrogen bond cleavage. The magnitude of the 4'-isotope effects for Fe.BLM ranges from 2 to 7 (+/- 0.3) and is not sensitive to changes in the partition ratio of the two proposed cleavage pathways. However, the isotope effect is sensitive to structural changes in BLM, such as with tallysomycin, and to changes in metal and cleavage mechanism, such as with Co.BLM. The variability of the effects are discussed in light of the factors responsible for the observation of V/K isotope effects. The findings suggest that the kinetics, thermodynamics, and geometry of carbon-hydrogen bond cleavage by Fe.BLM permit the observation of large isotope effects on this chemical step. Fe.BLM may be viewed, therefore, as a special case.

Base Sequence↗
PubMed1992

Bisintercalators of DNA with a rigid linker in an extended configuration.

A new class of DNA bisintercalators is reported in which phenanthridinium or acridinium rings are connected by rigid and extended linkers of varied length. Cross-linking of DNA by bisintercalation is inferred from the unwinding and folding of linear DNA induced by the compound; after ligation and removal of the bisintercalator, superhelical circles, catenanes, and knots that bear an imprint of the bisintercalator are observed. These novel bisintercalators are of interest because they can be used to probe the organization of DNA in three-dimensional space, especially near sites of replication, recombination, or topoisomerase action, where two duplexes must be in close proximity.

Acridines↗
PubMed1991

19F NMR studies of the D-galactose chemosensory receptor. 1. Sugar binding yields a global structural change.

The Escherichia coli D-galactose and D-glucose receptor is an aqueous sugar-binding protein and the first component in the distinct chemosensory and transport pathways for these sugars. Activation of the receptor occurs when the sugar binds and induces a conformational change, which in turn enables docking to specific membrane proteins. Only the structure of the activated receptor containing bound D-glucose is known. To investigate the sugar-induced structural change, we have used 19F NMR to probe 12 sites widely distributed in the receptor molecule. Five sites are tryptophan positions probed by incorporation of 5-fluorotryptophan; the resulting 19F NMR resonances were assigned by site-directed mutagenesis. The other seven sites are phenylalanine positions probed by incorporation of 3-fluorophenylalanine. Sugar binding to the substrate binding cleft was observed to trigger a global structural change detected via 19F NMR frequency shifts at 10 of the 12 labeled sites. Two of the altered sites lie in the substrate binding cleft in van der Waals contact with the bound sugar molecule. The other eight altered sites, specifically two tryptophans and six phenylalanines distributed equally between the two receptor domains, are distant from the cleft and therefore experience allosteric structural changes upon sugar binding. The results are consistent with a model in which multiple secondary structural elements, known to extend between the substrate cleft and the protein surface, undergo shifts in their average positions upon sugar binding to the cleft. Such structural coupling provides a mechanism by which sugar binding to the substrate cleft can cause structural changes at one or more docking sites on the receptor surface.

Carbohydrate Metabolism↗
PubMedDate not supplied

Escherichia coli host cell modifications in continuous culture affecting heterologous protein overproduction: a population dynamics study.

There are many published studies of plasmid segregational instability in Escherichia coli in the literature. However, the formation of plasmid-free segregants can be controlled by the addition of selective chemical agents like antibiotics. This solution has become commonplace in both the laboratory and industry. On the other hand, host cell modifications, which result in low production of plasmid-encoded protein and lead to loss of culture productivity, have not been adequately addressed. Continuous culture of an inducible (ptac) Escherichia coli vector containing strain, RB791(pKN), was characterized by strong dynamic changes in the cell population and product (beta-lactamase) expression. Long-term cultivation resulted in the loss of high-level production of beta-lactamase. Loss of productivity was not due to the formation of plasmid-free cells or structural modifications to the plasmid; instead, continuous operation resulted in a culture dominated by irreversibly altered, low-producing cells. Two distinct classes of lac- mutants which inhibited induction were identified (Y- and I(s)).

Chromosomes, Bacterial↗
PubMed2002

Digitoxosyltetracenomycin C and glucosyltetracenomycin C, two novel elloramycin analogues obtained by exploring the sugar donor substrate specificity of glycosyltransferase ElmGT.

Our explorations of glycosyltransferase ElmGT from Streptomyces olivaceus Tü 2353, which shows an interesting flexibility regarding its sugar donor substrate, were extended toward various previously unexplored sugar co-substrates. The studies revealed that ElmGT, which normally transfers L-rhamnose to 8-demethyltetracenomycin C as a crucial biosynthetic step in elloramycin biosynthesis, is also able to process an activated non-deoxygenated sugar, NDP-D-glucose, as well as NDP-L-digitoxose, which is the first example of an NDP-L-sugar co-substrate of ElmGT possessing an axial 3-OH group. The structures of the resulting novel elloramycin analogues of these experiments, 8-demethyl-8-L-digitoxosyltetracenomycin C (4) and 8-demethyl-8-D-glucosyltetracenomycin C (7), were elucidated mainly by (1)H and (13)C NMR spectroscopy and by mass spectrometry.

Anthraquinones↗
PubMed2003

Novel poly(amino ester)s obtained from Michael addition polymerizations of trifunctional amine monomers with diacrylates: safe and efficient DNA carriers.

Novel biodegradable poly(amino ester)s containing secondary and tertiary amines in the backbones were obtained from the Michael addition polymerizations of trifunctional amine monomers with diacrylates, and showed high transfection efficiency for the delivery of DNA comparable to those of polyethylenimine (PEI) and low cytotoxicity.

Acrylates↗
PubMed1994

Abnormalities of PIG-A transcripts in granulocytes from patients with paroxysmal nocturnal hemoglobinuria.

BACKGROUND: Paroxysmal nocturnal hemoglobinuria (PNH) is an acquired disorder in which there is a deficiency in the synthesis by hematopoietic cells of the glycosyl-phosphatidylinositol molecules that anchor proteins to the cell membrane. Recently, we demonstrated that a gene termed PIG-A (for phosphatidylinositol glycan class A), a component of glycosyl-phosphatidylinositol biosynthesis, was responsible for PNH in two patients. The present study was undertaken to elucidate whether PIG-A is the gene responsible for all cases of PNH and to characterize further the somatically acquired abnormalities of this gene. METHODS: We studied granulocytes from 15 patients with PNH. The cell content of CD55 and CD59 was assessed by fluorescence-activated flow cytometry. PIG-A transcripts were reverse-transcribed, amplified by the polymerase chain reaction, and cloned into plasmids. The structure of the cloned complementary DNA was analyzed by nucleotide sequencing, and its function was assessed on the basis of its ability to restore to normal the abnormal phenotype of a PIG-A-deficient cell line after transfection. RESULTS: Three patients had size abnormalities of PIG-A transcripts with different patterns, and in one patient a very low level of the PIG-A transcript was found. Eleven patients had transcripts of normal size, but the transfection assay revealed that in each patient some of them were nonfunctional. The percentage of nonfunctional PIG-A transcripts was correlated with the percentage of affected granulocytes (P < 0.001). Sequence analysis demonstrated somatic mutations in two of the patients. CONCLUSIONS: PIG-A is the gene responsible for PNH in all patients studied to date.

Base Sequence↗
PubMed1998

The natural polyamine spermine functions directly as a free radical scavenger.

The polyamines are small organic cations that are absolutely required for eukaryotic cell growth. Although their growth requirements are well established, the molecular functions of the polyamines are ill-defined. Oxidative damage to DNA by reactive oxygen species is a continual problem that cells must guard against to survive. The polyamine spermine, which is normally found in millimolar concentrations in the nucleus, is shown here to function directly as a free radical scavenger, and adducts formed as a result of this function are identified. These data suggest that spermine is a major natural intracellular compound capable of protecting DNA from free radical attack.

Azides↗
PubMed2001

Sticky DNA, a self-associated complex formed at long GAA*TTC repeats in intron 1 of the frataxin gene, inhibits transcription.

Friedreich's ataxia (FRDA) is an autosomal recessive neurodegenerative disease caused by the expansion of GAA.TTC repeats in the first intron of the frataxin (X25) gene. FRDA patients carrying two expanded GAA.TTC repeats show very low levels of mature frataxin mRNA and protein. A novel type of unusual DNA structure, sticky DNA, was previously found in the expanded GAA.TTC repeats from FRDA patients. To evaluate the effect of sticky DNA on transcription, in vitro transcription studies of (GAA.TTC)(n) repeats (where n = 9-150) were carried out using T7 or SP6 RNA polymerase. When a gel-isolated sticky DNA template was transcribed, the amount of full-length RNA synthesized was significantly reduced compared with the transcription of the linear template. Surprisingly, transcriptional inhibition was observed not only for the sticky DNA template but also another DNA molecule used as an internal control in an orientation-independent manner. The molecular mechanism of transcriptional inhibition by sticky DNA was a sequestration of the RNA polymerases by direct binding to the complex DNA structure. Moreover, plasmids containing the (GAAGGA.TCCTTC)(65) repeat, which does not form sticky DNA, did not inhibit in vitro transcription, as expected. These results suggest that the role of sticky DNA in FRDA may be the sequestration of transcription factors.

DNA↗
PubMed2003

Structural analysis of four large plasmids harboring in a unicellular cyanobacterium, Synechocystis sp. PCC 6803.

The genome of the unicellular cyanobacterium Synechocystis sp. PCC 6803 consists of a single chromosome and several plasmids of different sizes, and the nucleotide sequences of the chromosome and three small plasmids (5.2 kb, 2.4 kb, and 2.3 kb) have already been sequenced. We newly determined the nucleotide sequences of four large plasmids, which have been identified in our laboratory (pSYSM:120 kb, pSYSX:106 kb, pSYSA:103 kb, and pSYSG:44 kb). Computer-aided analysis was performed to explore the genetic information carried by these plasmids. A total of 397 potential protein-encoding genes were predicted, but little information was obtained about the functional relationship of plasmids to host cell, as a large portion of the predicted genes (77%) were of unknown function. The occurrence of the potential genes on plasmids was divergent, and parA was the only gene common to all four large plasmids. The distribution data of a Cyanobacterium-specific sequence (HIP1: 5'-GCGATCGC-3') suggested that respective plasmids could have originated from different cyanobacterial strains.

Base Sequence↗
PubMed1986

Structure- and sequence-specificity of ozone degradation of supercoiled plasmid DNA.

Ozone-reactive sites on the nucleobase moieties in supercoiled pBR322 DNA were investigated by using sequencing procedures. Ozonolysis in the absence of salt resulted in degradation of thymine residues in the A + T rich region located at 3100-3400bp. In the presence of salt, such as NaCl or MgCl2, a conformational change of plasmid DNA was induced. Subsequently the thymine and guanine residues in the loop of the cruciform located at 3120bp and 3220bp were degraded. In addition, central thymine residues present in sequences GTA, GTT and ATA were also degraded.

Base Sequence↗
PubMed1980

Structure of a promotor on plasmid pMB9 derived from plasmid pSC101.

The DNA sequence of a 354 basepair EcoRI-HindIII fragment of plasmid pMB9 which has originally been derived from plasmid pSC101 has been resolved. This fragment contains a promoter for transcription directed towards the EcoRI site. Escherichia coli RNA polymerase binds to a region within the EcoRI-HindIII fragment which contains the heptamer 5' TATGGTG (132-126) and the duodecamer 5' TGATGAACATCA (158-147). Based on commonalities with other promotors these DNA sequences probably function as, respectively, "binding site" and "recognition site". Furthermore, this fragment harbours a translation reading frame free of nonsense codons and at about 25 basepairs from the indicated heptamer a nucleotide sequence which meets with the requirements for initiation of translation. By heteroduplex mapping it was shown that the EcoRI-HindIII fragment has been derived from a region near or within the origin of replication of pSC101. The copynumber of plasmids containing the EcoRI-HindIII fragment is two-fold lower than that of plasmids lacking this fragment. This effect might be related to the original function of this fragment on plasmid pSC101.

Base Sequence↗
PubMed1995

Deletion analysis of the starch-binding domain of Aspergillus glucoamylase.

The large form of glucoamylase (GAI) from Aspergillus awamori (EC 3.2.1.3) binds strongly to native granular starch, whereas a truncated form (GAII) which lacks 103 C-terminal residues, does not. This C-terminal region, conserved among fungal glucoamylases and other starch-degrading enzymes, is part of an independent starch-binding domain (SBD). To investigate the SBD boundaries and the function of conserved residues in two putative substrate-binding sites, five gluco-amylase mutants were constructed with extensive deletions in this region for expression in Saccharomyces cerevisiae. Progressive loss of both starch-binding and starch-hydrolytic activity occurred upon removal of eight and 25 C-terminal amino acid residues, or 21 and 52 residues close to the N-terminus, confirming the requirement for the entire region in formation of a functional SBD. C-terminal deletions strongly impaired SBD function, suggesting a more important role for one of the putative binding sites. A GAII phenocopy showed a nearly complete loss of starch-binding and starch-hydrolytic activity. The deletions did not affect enzyme activity on soluble starch or thermo-stability of the enzyme, confirming the independence of the catalytic domain from the SBD.

Amino Acid Sequence↗