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PubMed2004

Concurrent targeted exchange of three bases in mammalian hprt by oligonucleotides.

The repair of point mutations in hprt gene by single-stranded oligonucleotides represents a model to test targeted nucleotide exchange. We studied the concurrent nucleotide exchange of two or three nucleotides in the hprt deficient hamster cell line V79-151. The used oligonucleotides resulted in mismatches at two (151, 159) or three (151, 144, and 159) hprt positions. The hprt point mutation at position 151 was repaired in about 2/10(6) cells as shown by hprt sequencing in clones surviving HAT selection. The second nucleotide exchange at hprt position 159 was found in 7% of these HAT selected clones. Using oligonucleotides resulting in three mismatches, 29% of the clones showed nucleotide exchanges at the two hprt positions (151, 144) and about 4% at three positions (151, 144, and 159). These results indicate that single-stranded oligonucleotides can generate two or three nucleotide exchanges in a mammalian chromosomal gene.

Amino Acid Sequence↗

PubMed1995

Multiple forms of mouse PG-M, a large chondroitin sulfate proteoglycan generated by alternative splicing.

We have isolated and sequenced cDNA clones that encode the core protein of PG-M-like proteoglycan produced by cultured mouse aortic endothelial cells (Morita, H., Takeuchi, T., Suzuki, S., Maeda, K., Yamada, K., Eguchi, G., and Kimata, K. (1990) Biochem. J. 265, 61-68). A homology search of the cDNA sequence has suggested that the core protein is a mouse equivalent of chick PG-M(V1), one of the alternatively spliced forms of the PG-M core protein, which may correspond to human versican. Northern blot analysis revealed three mRNA species of 10, 9, and 8 kilobases (kb) in size. The analysis of PG-M mRNA species in embryonic limb buds and adult brain revealed the presence of other mRNA species with different sizes; the one with the largest size (12 kb) was found in embryonic limb buds, and the ones with smaller sizes of 7.5 and 6.5 kb were in adult brain. Sequencing of cDNA clones for the smaller forms in the adult brain showed that they were different from PG-M(V1) in encoding the second chondroitin sulfate attachment domain (CS alpha) alone. Occurrence of the PCR products striding over the junction of the first and second chondroitin sulfate attachment domains suggested that a mRNA of 12 kb in size corresponded to a transcript without the alternative splicing (PG-M(V0)). It is likely, therefore, that multiforms of the PG-M core protein may be generated by alternative usage of either or both of the two different chondroitin sulfate attachment domains (alpha and beta) and that molecular forms of PG-M may vary from tissue to tissue by such an alternative splicing.

Alternative Splicing↗

PubMed1997

Amino acid differences in the N-terminus of C(H)2 influence the relative abilities of IgG2 and IgG3 to activate complement.

The four human IgG isotypes are highly conserved in amino acid sequence, but show differential ability to activate complement (C'): IgG3 and IgG1 are very active, IgG2 is active under certain conditions, and IgG4 is inactive. Although the second constant domain [C(H)2] is critical for C' activation, the individual amino acids that confer isotype-specific activity have not been identified. We have generated a series of mutants between IgG2 and IgG3, resulting in the exchange of the four N-terminal and six C-terminal polymorphic residues within C(H)2. Mutants containing the N-terminus of the C(H)2 of IgG3 were as effective as wildtype IgG3 in C1q binding, C1 activation and terminal complex (MAC) formation, but had reduced ability to effect C'-mediated lysis. IgG2 and mutants containing the N-terminal portion of the C(H)2 of IgG2 were reduced compared to IgG3 in activating C1, binding C1q and inducing assembly of the MAC, and were inactive in mediating lysis of target cells. Thus, the amino acid sequence differences in the N-terminus of C(H)2 play a critical role in determining the relative abilities of IgG2 and IgG3 to bind C1q and activate the C' cascade although additional residues of C(H)2 must be involved in mediating optimal target cells lysis. The sequence of the N-terminus of C(H)2 was less critical in determining C4 and C3 binding. Characterization of domain exchange mutants suggests that intermediate steps may be partly dependent on domains other than C(H)2. IgGs that do not direct target cell lysis nevertheless activate intermediate steps in the pathway, which may contribute to immune complex-associated disorders.

Amino Acid Sequence↗

PubMed2002

Spongistatin synthetic studies. An efficient, second-generation construction of an advanced ABCD intermediate.

[reaction: see text] A short, efficient, and stereocontrolled synthesis of (-)-4, an advanced ABCD subunit of the spongistatins, has been achieved. Central to the synthetic strategy is the multicomponent linchpin union of silyl dithianes with epoxides to access both the AB and CD fragments. Fragment coupling was then achieved via an efficient stereoselective aldol reaction. The linear sequence required 22 steps and proceeded in 4.0% overall yield.

Animals↗

PubMed1997

In vivo metabolic profile of a phosphorothioate oligodeoxyribonucleotide.

Antisense phosphorothioate oligodeoxyribonucleotides (PS oligonucleotides) have the ability to inhibit individual gene expression in the potential treatment of cancer and viral diseases. Following administration in vivo, PS oligonucleotides are rapidly cleared from the plasma and distributed to various organs. However, the manner in which administered oligonucleotides are metabolized in plasma and tissues is poorly understood. In this study, a 25-mer PS oligonucleotide (GEM91) complementary to the gag gene mRNA of the human immunodeficiency virus (HIV-1) was administered to mice through intravenous injections to investigate its metabolism. The PS oligonucleotide was extracted from plasma at 1 hour postadministration and from kidney and liver at 24 hours postadministration. After extraction, the PS oligonucleotide and its metabolites were tailed with dA and annealed to a dT-tailed plasmid. The recombinant plasmid was ligated and used to transform competent bacteria. The region of interest containing the PS oligonucleotide was then sequenced. Our results show that degradation of the PS oligonucleotide in plasma was primarily from the 3'-end. However, in kidney and liver, degradation was primarily from the 3'-end, but a large proportion of the PS oligonucleotide was degraded from the 5'-end as well. We also studied the metabolism of PS oligonucleotide in plasma after 2-hour intravenous infusion in HIV-infected patients. The degradation of the PS oligonucleotide in plasma was primarily from the 3'-end. This study is important in understanding the metabolism of antisense PS oligonucleotide in vivo in general but also provides guidance for designing second-generation antisense oligonucleotides with improved stability and safety profile.

Animals↗

PubMed1997

Sequence patterns indicate an enzymatic involvement in integration of mammalian retroposons.

It is commonly accepted that the reverse-transcribed cellular RNA molecules, called retroposons, integrate at staggered breaks in mammalian chromosomes. However, unlike what was previously thought, most of the staggered breaks are not generated by random nicking. One of the two nicks involved is primarily associated with the 5'-TTAAAA hexanucleotide and its variants derived by a single base substitution, particularly A --> G and T --> C. It is probably generated in the antisense strand between the consensus bases 3'-AA and TTTT complementary to 5'-TTAAAA. The sense strand is nicked at variable distances from the TTAAAA consensus site toward the 3' end, preferably within 15-16 base pairs. The base composition near the second nicking site is also nonrandom at positions preceding the nick. On the basis of the observed sequence patterns it is proposed that integration of mammalian retroposons is mediated by an enzyme with endonucleolytic activity. The best candidate for such enzyme may be the reverse transcriptase encoded by the L1 non-long-terminal-repeat retrotransposon, which contains a freshly reported domain homologous to the apurinic/apyrimidinic (AP) endonuclease family [Martin, F., Olivares, M., Lopez, M. C. & Alonso, C. (1996) Trends Biochem. Sci. 21, 283-285; Feng, Q., Moran, J. V., Kazazian, H. H. & Boeke, J. D. (1996) Cell 87, 905-916] and shows nicking in vitro with preference for targets similar to 5'-TTAAAA/3'-AATTTT consensus sequence [Feng, Q., Moran, J. V., Kazazian, H. H. & Boeke, J. D. (1996) Cell 87, 905-916]. A model for integration of mammalian retroposons based on the presented data is discussed.

Animals↗

PubMed2003

Analysis of high mass peptides using a novel matrix-assisted laser desorption/ionisation quadrupole ion trap time-of-flight mass spectrometer.

A novel matrix-assisted laser desorption/ionisation quadrupole ion trap time-of-flight (MALDI QIT ToF) mass spectrometer has been used to analyse high mass peptide ions exceeding 2000 Da. Human adrenocorticotropic hormone (fragment 18-39) and oxidised bovine insulin chain B were utilised to evaluate the performance of the instrument both in MS and in MS/MS mode. Its ability to efficiently isolate ions and to fragment them using collisionally activated decomposition (CAD) has been demonstrated using mixtures diluted to the low-femtomole level on target. Additionally, multiple stage mass spectrometry (MS/MS/MS) provides a second-generation product ion spectrum in which new fragment ions are detected and new stretches of amino acids are identified.

Adrenocorticotropic Hormone↗

PubMed2003

Monopolar spindle attachment of sister chromatids is ensured by two distinct mechanisms at the first meiotic division in fission yeast.

At meiosis I, sister chromatids attach to the same spindle pole (i.e. monopolar attachment). Mechanisms establishing monopolar attachment remain largely unknown. In the fission yeast Schizosaccharomyces pombe, monopolar attachment is established in haploid cells, indicating that homologous chromosomes are dispensable for its establishment. This monopolar attachment requires both mating pheromone signaling and inactivation of Pat1 kinase (a key negative regulator of meiosis). It also requires the meiotic cohesin factor Rec8 but not the recombination factor Rec12. In contrast, in diploid cells, monopolar attachment is established by Pat1 inactivation alone, and does not require mating pheromone signaling. Furthermore, monopolar attachment requires Rec12 in addition to Rec8. These results indicate that monopolar attachment of sister chromatids can be established by two distinct mechanisms in S.pombe, one that is pheromone dependent and recombination independent, and a second that is pheromone independent and recombination dependent. We propose that co-operation of these two mechanisms generates the high fidelity of monopolar attachment.

Base Sequence↗

PubMed1994

Inhibition of G protein-coupled receptor signaling by expression of cytoplasmic domains of the receptor.

The third intracellular domain (3i) of G protein-coupled receptors plays a major role in the activation of G proteins. Alterations in this region of the receptor can affect receptor/G protein coupling efficiency and specificity. We recently reported (Luttrell, L. M., Cotecchia, S., Ostrowski, J., Kendall, H., Lefkowitz, R.J. (1993) Science 259, 1453-1457) that coexpression of the 3i domain of the alpha 1B adrenergic receptor (AR) (alpha 1B3i) specifically inhibited alpha 1BAR-mediated inositol phosphate production, with no effect on D1A dopamine receptor (D1ADR)-mediated cAMP production. Similarly, expression of the 3i domain of D1ADR (D1A3i) inhibited D1ADR-mediated cAMP production but did not affect alpha 1BAR-mediated inositol phosphate accumulation. This suggests that peptides derived from a G protein-coupled receptor might serve as antagonists of receptor/G protein interactions. The present studies were performed to test the generality as well as the specificity of this phenomenon. The effect of expression of the second intracellular domain (2i), the 3i domain, and the fourth intracellular domain (4i) of alpha 1BAR on second messenger generation mediated by the alpha 1BAR, the M1 muscarinic cholinergic receptor (M1AChR), and the D1ADR was examined. Although the alpha 1B2i domain had no effect on receptor/G protein coupling for any receptor tested, the alpha 1B3i domain inhibited signaling mediated by alpha 1BAR and M1AChR but not by D1ADR, while the alpha 1B4i domain inhibited signaling mediated by each of the receptors. To investigate the generality of 3i domain-induced inhibition of receptor activity further, the 3i domains of two Gq-coupled receptors (alpha 1BAR and M1AChR) and two Gi-coupled receptors (alpha 2AAR and M2AChR) were tested for effects on the second messenger generation mediated by each of the four receptors. In each case, the homologous 3i domain caused significant inhibition (40-60%), while the 3i domain of the receptor coupled to the same G protein also decreased receptor/G protein coupling. In contrast, receptor/G protein coupling appeared unaffected by expression of 3i domains derived from receptors coupled to different G proteins. The alpha 1B3i domain-provoked inhibition of homologous receptor signaling was surmountable at high receptor density, and assays using a phorbol response element/reporter gene construct detected a weak enhancement of basal second messenger generation in cells expressing the alpha 1B3i domain alone.(ABSTRACT TRUNCATED AT 400 WORDS)

Amino Acid Sequence↗

PubMed1999

Intensity-modulation radiotherapy using independent collimators: an algorithm study.

The purpose of this work is to investigate algorithms for the delivery of intensity-modulated fields using independent collimators (IC). Two heuristic algorithms are proposed to calculate jaw-setting sequences for arbitrary 2D intensity distributions. The first algorithm is based on searching the whole intensity matrix to find the largest nonzero rectangular area as a segment while the second algorithm is to find a nonzero rectangular area as a segment which makes the complexity of the remaining intensity matrix minimum. After a sequence is obtained, the delivery order of all its segments is optimized with the technique of simulated annealing to minimize the total jaw-moving time. To evaluate these two algorithms, randomly generated intensity matrices and three clinical cases of different complexity have been tested, and the results have been compared with one algorithm proposed for MLC technique. It is shown that the efficiency of IC technique becomes increasingly lower than that of MLC technique, and the relative efficiency of two algorithms proposed here is related to machine dose rate and jaw speed. Assuming the prescribed dose is 200 cGY per fraction, machine dose rate is 250 MU/min, and jaw speed is 1.5 cm/s, the treatment can be delivered within about 20 min for all three cases with the first algorithm. The second algorithm requires longer delivery time under such assumptions. The delivery time can be further reduced through increasing machine dose rate and jaw speed, and developing more efficient algorithms. The use of IC for intensity-modulation radiotherapy has some potential advantages over other techniques.

Algorithms↗

PubMed1990

Construction of a novel artificial-ribozyme-releasing plasmid.

A novel 'active-ribozyme-releasing system' was constructed, taking advantage of the consensus sequence of a new class of ribozyme. An active ribozyme sequence, targeted for the SFL1 gene (a yeast suppressor gene for flocculation) was fused just downstream of the T7 promoter. The 3' terminus of the first ribozyme was designed to be trimmed by the second ribozyme connected to the downstream of the first active ribozyme. In vitro experiments revealed that the active ribozyme targeted to SFL1 was successfully released by the action of the second ribozyme, subsequently cleaving the SFL1 mRNA at the predetermined site. Since the first active ribozyme with a defined 3'-terminus can be produced even when a circular DNA is used as a template, this kind of construct has a potential to release an 'active ribozyme' tailored to destroy a target gene (RNA) in vivo. Moreover, the second ribozyme in this construct can be utilized as a universal pseudo-terminator for generation of any RNA transcripts inserted in place of the cassette portion of the first ribozyme.

Base Sequence↗

PubMed2002

Immunologic and genetic characterization of lipooligosaccharide variants in a Neisseria meningitidis serogroup C strain.

Neisseria meningitidis shows great variation in expression of structurally different lipooligosaccharides (LOS) on its cell surface. To better understand the LOS diversity that may occur within an individual strain, a group C wild-type strain, BB305-Tr4, and two stable isogenic LOS variants, Tr5 and Tr7, were selected for this study. SDS-PAGE analysis showed a size reduction of Tr5 and Tr7 LOS compared to that of Tr4. Immunoblotting showed that parental Tr4 LOS reacted with L1, L2 and L3,7 antibodies, variant Tr5 LOS with L1 and L6 antibodies, while Tr7 LOS was non-typeable. Genetic analysis showed that the gene organization at the lgt-1 locus in the three strains was lgtZ,C,A,B,H4 in Tr4, lgtZ,C,A,H4 in Tr5 and lgtZ,C,A,H9 in Tr7. The genetic differences in the three strains were consistent with their phenotypic changes. Sequence comparison revealed two independent recombination events. The first was the recombination of repeated DNA fragments in the flanking regions to delete lgtB in Tr5. The second was the recombination of a fragment of two genes, lgtB and lgtH4, to create an inactive lgtH9 allele with a mosaic structure in Tr7. These findings suggest that besides phase variation, homologous recombination can contribute to the genetic diversity of the lgt locus and to the generation of LOS variation in N. meningitidis.

Base Sequence↗

PubMed1988

The HeLa cell protein TEF-1 binds specifically and cooperatively to two SV40 enhancer motifs of unrelated sequence.

We have purified a protein (TEF-1) that specifically binds to two sequence unrelated motifs (GT-IIC and Sph) of the simian virus 40 (SV40) enhancer. TEF-1 binds cooperatively to templates containing tandem but not inverted or spaced repeats of its cognate motifs. This cooperative binding correlates with the ability of the tandem repeats to generate enhancer activity in vivo. In contrast, TEF-1 and a second SV40 enhancer binding protein, TEF-2, bind independently to templates containing the cognate motifs of both proteins (GT-I and either GT-IIC or Sph motifs) even though these motifs cooperate in enhancer activity in vivo. These results allow us to distinguish different classes of enhancer factors.

Allosteric Regulation↗

PubMed2001

The second EF-hand is responsible for the isoform-specific sorting of myosin essential light chain.

It has been known that isoforms of myosin essential light chain (LC) exhibit the isoform-specific sorting within cardiac myocytes and fibroblasts. In order to analyze which domain of LC is responsible for the sorting, various chimeric cDNA constructs between human nonmuscle isoform (LC3nm) and chicken fast skeletal muscle isoform (LC3f) were generated and expressed in cultured chicken cardiac myocytes. If chimeras contained LC3f sequence at the place that was restricted by BssHII and PstI, they were preferentially sorted to sarcomeres and precisely localized at A-bands, and their incorporation levels into the A-bands were identical with that of the wild type LC3f. However, other chimeras were distributed throughout the cytoplasm like the wild type LC3nm. Comparison of amino acid sequences revealed that 12 amino acids are different between chicken LC3f and human LC3nm in the BssHII-PstI fragment, and these amino acids are located within the second EF-hand of LC. These results indicated that the second EF-hand is responsible for the isoform-specific sorting of LC. Although the second EF-hand is not included in the key contacts with myosin heavy chain, it is supposed that this domain is important for the relative disposition of neighboring domains. Thus, the 12 amino acids in the second EF-hand might play a key role for modulation of overall configuration of LC, thereby influencing the precise association of the key contacts.

Amino Acid Sequence↗

PubMed2001

Characterization and reduction of the transient response in steady-state MR imaging.

Refocused steady-state free precession (SSFP) imaging sequences have recently regained popularity as faster gradient hardware has allowed shorter repetition times, thereby reducing SSFP's sensitivity to off-resonance effects. Although these sequences offer fast scanning with good signal-to-noise efficiency, the "transient response," or time taken to reach a steady-state, can be long compared with the total imaging time, particularly when using 2D sequences. This results in lost imaging time and has made SSFP difficult to use for real-time and cardiac-gated applications. A linear-systems analysis of the steady-state and transient response for general periodic sequences is shown. The analysis is applied to refocused-SSFP sequences to generate a two-stage method of "catalyzing," or speeding up the progression to steady-state by first scaling, then directing the magnetization. This catalyzing method is compared with previous methods in simulations and experimentally. Although the second stage of the method exhibits some sensitivity to B(1) variations, our results show that the transient time can be significantly reduced, allowing imaging in a shorter total scan time. Magn Reson Med 46:149-158, 2001.

Humans↗

PubMed1987

Prediction of the tertiary structure of the alpha-subunit of tryptophan synthase.

The tertiary structure of the alpha-subunit of tryptophan synthase was proposed using a combination of experimental data and computational methods. The vacuum-ultraviolet circular dichroism spectrum was used to assign the protein to the alpha/beta-class of supersecondary structures. The two-domain structure of the alpha-subunit (Miles et al.: Biochemistry 21:2586, 1982; Beasty and Matthews: Biochemistry 24:3547, 1985) eliminated consideration of a barrel structure and focused attention on a beta-sheet structure. An algorithm (Cohen et al.: Biochemistry 22:4894, 1983) was used to generate a secondary structure prediction that was consistent with the sequence data of the alpha-subunit from five species. Three potential secondary structures were then packed into tertiary structures using other algorithms. The assumption of nearest neighbors from second-site revertant data eliminated 97% of the possible tertiary structures; consideration of conserved hydrophobic packing regions on the beta-sheet eliminated all but one structure. The native structure is predicted to have a parallel beta-sheet flanked on both sides by alpha-helices, and is consistent with the available data on chemical cross-linking, chemical modification, and limited proteolysis. In addition, an active site region containing appropriate residues could be identified as well as an interface for beta 2-subunit association. The ability of experimental data to facilitate the prediction of protein structure is discussed.

Amino Acid Sequence↗

PubMed1995

Peroxisomal membrane protein PMP68 of mouse liver: cloning of a cDNA encompassing the nucleotide binding fold and epitope mapping of monoclonal antibodies to the expressed protein.

We have isolated and sequenced a cDNA which encodes 376 amino acids toward the carboxy-terminus, and encompassing the putative nucleotide binding fold, of PMP68 (mouse liver peroxisomal integral membrane protein of 68 kDa) the major integral membrane protein of mouse liver peroxisomes. The protein sequence predicted from this cDNA shows 97.9% amino acid identity to this same region of rat liver PMP70, a member of the ATP-binding cassette protein superfamily (K. Kamijo, S. Taketani, S. Yokota, T. Osumi, and T. Hashimoto, 1990, J. Biol. Chem. 265, 4534-4540). The section of the cDNA encoding the hydrophilic and putative cytoplasmic domain of PMP68 was expressed as a recombinant fusion protein in bacteria. Two monoclonal antibodies raised against this protein have been epitope-mapped to peptides generated by cyanogen bromide cleavage of the fusion protein. Antibody 1A4 recognizes a peptide whose sequence contains the first motif of the putative nucleotide binding fold of PMP68, and antibody 8F11 recognizes a carboxy-terminal peptide which includes the second motif of this nucleotide binding fold. These antibodies are expected to be useful in the elucidation of the biological function of this putative membrane transporter.

ATP-Binding Cassette Transporters↗

PubMed1988

Botulinum neurotoxin type A: cleavage of the heavy chain into two halves and their partial sequences.

The 145-kDa type A botulinum neurotoxin (NT) is produced by the bacteria Clostridium botulinum (strain, Hall). The heavy (H) and light (L) chains (97- and 53-kDa, respectively) of this protein are linked by at least one disulfide bond. The N- and C-terminal halves of the H chain appear to have different functions in the mechanism of action of the NT [1987) FEBS Lett. 226, 115-120). Well-characterized and highly purified preparations of the two halves of the H chain are needed for such studies. Two different approaches were taken to cut the H chain with trypsin and isolate the fragments. In one method the cleavage products were: (i) 94-kDa fragment made of the L chain linked to the N-terminal half of the H chain (49 kDa) by a disulfide bond(s), and (ii) the C-terminal 44-kDa fragment. The N-terminal half of H chain was separated from the L chain by reducing the disulfide bond(s) linking them and then purified by ion-exchange chromatography. The 1-27 residues of 49-kDa N-terminal half of the H chain were Ala-Leu-Asn-Asp-Leu-Cys-Ile-Lys-Val-Asn-Asn-Trp-Asp-Leu-Phe-Phe-Ser-Pro- Ser-Glu - Asp-Asn-Phe-Thr-Asn-Asp-Leu-. The sequence of the other half of the H chain (44 kDa) was X-Ile-Ile-Asn-Leu-X-Ile-Leu-Asn-Leu-Arg-Tyr-Glu-X-Asn-His-Leu-Ile-Asp-Le u-Lys- X-Tyr-Ala-Ser-. In the second method, the H chain was first separated from the L chain, purified, and then cleaved. One product of cleavage, the 44-kDa fragment, was partially sequenced; the first 25 residues were identical to the sequence of the 44-kDa fragment generated by the first method. The present work also demonstrated that (i) The cysteine residue(s) located on the N-terminal half of the H chain form the -S-S- link(s) with the L chain. (ii) The other half of the H chain (44-kDa fragment, apparently the C-terminal half) is not linked via -S-S- to the L-chain or to the N-terminal half (49-kDa fragment) of the H chain.(ABSTRACT TRUNCATED AT 400 WORDS)

Amino Acid Sequence↗