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PubMed2003

Neuroblastoma directed therapy by a rational prodrug design of etoposide as a substrate for tyrosine hydroxylase.

Tumor directed cytotoxic therapy is one of the major challenges for the success of chemotherapy. In order to accomplish this goal in neuroblastoma, we rationally designed a prodrug of etoposide as substrate for tyrosine hydroxylase, a well established neuroblastoma associated enzyme. Here, we report synthesis and characterization of a 3,4 dihydroxy-phenyl carbamate derivative of etoposide. In order to demonstrate activation by tyrosine hydroxylase, the coding sequence of murine tyrosine hydroxylase was generated by reverse transcriptase-polymerase chain reaction from NXS2 neuroblastoma cells and cloned into the pRSET-A bacterial expression vector. The enzyme was expressed in Escherichia coli, characterized by Western blot and enzymatic activity was demonstrated by conversion of tyrosine into DOPA in the presence of cofactors using reversed phase high-performance liquid chromatography. Under these enzymatic conditions, we demonstrate conversion of 3,4 dihydroxy-phenyl carbamate prodrug into free etoposide. This effect was clearly mediated by the enzyme since bacteria transformed with the empty vector were ineffective of prodrug activation. Furthermore, tyrosine hydroxylase positive cells exposed to the etoposide prodrug were effectively killed in contrast to tyrosine hydroxylase negative controls. These findings demonstrate that etoposide can be designed as a prodrug substrate for tyrosine hydroxylase and thereby establish proof of concept for neuroblastoma directed enzyme prodrug therapy.

Animals↗

PubMed2003

Bacterial expression, purification, and characterization of rat kidney-type mitochondrial glutaminase.

The human gene that encodes the kidney-type glutaminase (KGA) spans 84-kb, contains 19 exons, and encodes two alternatively spliced mRNAs. Various segments of the rat KGA cDNA were PCR amplified and cloned into a bacterial expression vector to determine whether the N- and C- terminal ends of the glutaminase protein were essential for activity. A recombinant glutaminase, lacking the coding sequence contained in exon 1, was found to be fully active. In contrast, proteins that lacked sequences from exons 1 and 2 and exons 1-3 were inactive. An additional construct that corresponded to the sequence encoded by exons 2-14 also retained full activity. Both of the fully active, truncated proteins were purified to apparent homogeneity using an incorporated N-terminal His(6)-tag and Ni(2+)-affinity chromatography. The K(M) values for glutamine of the native and recombinant forms of glutaminase were nearly identical. However, the two truncated forms of the glutaminase exhibit the characteristic phosphate activation profile only when dialyzed into a buffer lacking phosphate. Dialysis versus 10mM Tris-phosphate was sufficient to form an active tetramer. Thus, the deleted N-terminal sequence may contribute to the phosphate-dependent oligomerization and activation of the native glutaminase.

Animals↗

PubMed2000

A broad-host-range expression vector series including a Ptac test plasmid and its application in the expression of the dod gene of Serratia marcescens (coding for ribulose-5-phosphate 3-epimerase) in Pseudomonas stutzeri.

A series of expression vectors for gram-negative bacteria was constructed which combine broad-host-range, inducible expression from the tac promoter and diverse antibiotic resistance determinants. The tac promoter activity and the repression by lacIq can be quantitated with a separate test plasmid in the strain to be studied. The dod gene of Serratia marcescens was expressed in Pseudomonas stutzeri and was shown to code for D-ribulose-5-phosphate 3-epimerase.

Bacterial Proteins↗

PubMed1984

cis-acting mutations that affect rop protein control of plasmid copy number.

A number of pMB1 derivatives provide a trans-acting function that can suppress lethal runaway replication of a temperature-sensitive copy-number mutant of NTP1. Deletion analysis indicates that the region of the pMB1 genome that contains the rop gene is required for this suppression. Mutant derivatives of the temperature-sensitive copy-number mutant plasmid whose conditional lethal phenotype is not suppressed in trans by the region encoding the rop gene have been isolated. These rop-insensitive derivatives contain single nucleotide changes within the RNA I coding region.

Bacterial Proteins↗

PubMed1995

Molecular cloning of a cDNA encoding human spermine synthase.

We have isolated and sequenced cDNA clones that encode human spermine synthase (EC 2.5.1.22). The total length of the sequenced cDNA was 1,612 nucleotides, containing an open reading frame encoding a polypeptide chain of 368 amino acids. All of the previously sequenced peptide fragments of human and bovine spermine synthase proteins could be located within the coding region derived from the cDNA. An unusual sequence of AATTAA apparently signaled the initiation of polyadenylation. Sequence comparisons between human spermine synthase and spermidine synthases from bacterial and mammalian sources revealed a nearly complete lack of similarity between the primary structures of these two enzymes catalyzing almost identical reactions. A modest similarity found was restricted to a relatively short peptide domain apparently involved in the binding of decarboxylated S-adenosylmethionine, the common substrate for both enzymes. The apparent lack of an overall similarity may indicate that spermine synthase, the enzyme found only in eukaryotes, and spermidine synthase with more universal distribution, although functionally closely related, have evolved separately.

Amino Acid Sequence↗

PubMed2004

Identification and distribution of new insertion sequences in the genome of the extremely halotolerant and alkaliphilic Oceanobacillus iheyensis HTE831.

Six kinds of new insertion sequences (ISs), IS667 to IS672, a group II intron (Oi.Int), and an incomplete transposon (Tn852loi) were identified in the 3,630,528-bp genome of the extremely halotolerant and alkaliphilic Oceanobacillus iheyensis HTE831. Of 19 ISs identified in the HTE831 genome, 7 were truncated, indicating the occurrence of internal rearrangement of the genome. All ISs except IS669 generated a 4- to 8-bp duplication of the target site sequence, and these ISs carried 23- to 28-bp inverted repeats (IRs). Sequence analysis revealed that four ISs (IS669, IS670, IS671, and IS672) were newly identified as belonging to separate IS families (IS200/IS605, IS30, IS5, and IS3, respectively). IS667 and IS668 were also characterized as new members of the ISL3 family. Tn8521oi, which belongs to the Tn3 family as a new member, generated a 5-bp duplication of the target site sequence and carried complete 38-bp IRs. Of the eight protein-coding sequences (CDSs) identified in Tn8521oi, three CDSs (OB481, OB482, and OB483) formed a ger gene cluster, and two other paralogous gene clusters were found in the HTE831 genome. Most of the ISs and the group II intron widely distributed throughout the genome were inserted in noncoding regions, while two ISs (IS667-08 and IS668-02) and Oi.Int-04 were inserted in the coding regions.

Amino Acid Sequence↗

PubMed1990

De novo purine nucleotide biosynthesis: cloning of human and avian cDNAs encoding the trifunctional glycinamide ribonucleotide synthetase-aminoimidazole ribonucleotide synthetase-glycinamide ribonucleotide transformylase by functional complementation in E. coli.

The trifunctional enzyme encoding glycinamide ribonucleotide synthetase (GARS)-aminoimidazole ribonucleotide synthetase (AIRS)-glycinamide ribonucleotide transformylase (GART) was cloned by functional complementation of an E. coli mutant using an avian liver cDNA expression library. In E. coli, genes encoding these separate activities (purD, purM, and purN, respectively) produce three proteins. The avian cDNA, in contrast, encodes a single polypeptide with all three enzyme activities. Using the avian DNA as a probe, a cDNA encoding the complete coding sequence of the trifunctional human enzyme was also isolated and sequenced. The deduced amino acid sequence of the human and avian polyproteins show extensive sequence homologies to the bacterial purD, purM, and purN encoded proteins. Avian and human liver RNAs appear to encode both a trifunctional enzyme (G-ARS-AIRS-GART) as well as an RNA which encodes only GARS. The trifunctional protein has been implicated in the pathology of Downs Syndrome and molecular tools are now available to explore this hypothesis. Initial efforts to compare the expression of GARS-AIRS-GART between a normal fibroblast cell line and a Downs Syndrome cell line indicate that the levels of RNA are similar.

Acyltransferases↗

PubMed2004

Temperature-dependent processing of the cspA mRNA in Rhodobacter capsulatus.

The expression of genes for cold-shock proteins is proposed to be regulated primarily at the post-transcriptional level by increase of mRNA stability after transition to low temperatures. Destabilization of the Escherichia coli cold-induced cspA transcript at 37 degrees C as well as stabilization upon cold shock is known to depend on the unusually long (159 nt) 5'-untranslated region. Determination of the cspA mRNA 5'-end from Rhodobacter capsulatus revealed a shorter distance between the start of transcription and the start codon for translation. The cspA mRNA of R. capsulatus was shown to be stabilized at low temperatures to a greater extent than other investigated transcripts. To address the mechanism of decay of the cspA transcript, it was incubated with purified degradosome of R. capsulatus. Endoribonucleolytic in vitro cleavage in the 5'-untranslated region as reported for the cspA transcript of E. coli in vivo was not observed. Instead, the data indicated that the cspA mRNA decay in R. capsulatus is mediated by endoribonucleolytic cleavages within the cspA coding region.

5' Untranslated Regions↗

PubMed1991

Isolation and properties of the RepA1 protein of the IncFII replicon, RepFIC.

The initiator protein RepA1 of the IncFII replicon RepFIC derived from the enterotoxin plasmid EntP307 has been cloned under the control of the lambda PL promoter. This has enabled us to overproduce this protein and study its properties. Here we show that RepA1 is a soluble basic protein with an experimentally determined molecular weight of 40,000. Deletion analysis indicates that the overproduced protein originates from the open reading frame which we previously designated as coding for RepA1. We have also shown that the replication function of the replicon RepFIC depends on the intact RepA1 coding frame.

Amino Acid Sequence↗

PubMed1989

L-, P-, and M-ring proteins of the flagellar basal body of Salmonella typhimurium: gene sequences and deduced protein sequences.

The flgH, flgI, and fliF genes of Salmonella typhimurium encode the major proteins for the L, P, and M rings of the flagellar basal body. We have determined the sequences of these genes and the flgJ gene and examined the deduced amino acid sequences of their products. FlgH and FlgI, which are exported across the cell membrane to their destinations in the outer membrane and periplasmic space, respectively, both had typical N-terminal cleaved signal-peptide sequences. FlgH is predicted to have a considerable amount of beta-sheet structure, as has been noted for other outer membrane proteins. FlgI is predicted to have an even greater amount of beta-structure. FliF, as is usual for a cytoplasmic membrane protein of a procaryote, lacked a signal peptide; it is predicted to have considerable alpha-helical structure, including an N-terminal sequence that is likely to be membrane-spanning. However, it had overall a quite hydrophilic sequence with a high charge density, especially towards its C terminus. The flgJ gene, immediately adjacent to flgI and the last gene of the flgB operon, encodes a flagellar protein of unknown function whose deduced sequence was hydrophilic and may correspond to a cytoplasmic protein. Several aspects of the DNA sequence of these genes and their surrounds suggest complex regulation of the flagellar gene system. A notable example occurs within the flgB operon, where between the end of flgG (encoding the distal rod protein of the basal body) and the start of flgH (encoding the L-ring protein) there was an unusually long noncoding region containing a potential stem-loop sequence, which could attenuate termination of transcription or stabilize part of the transcript against degradation. Another example is the interface between the flgB and flgK operons, where transcription termination of the former may occur within the coding region of the latter.

Amino Acid Sequence↗

PubMed1992

Molecular characterization of the dnaK gene region of Clostridium acetobutylicum, including grpE, dnaJ, and a new heat shock gene.

The dnaK gene region of Clostridium acetobutylicum was cloned in Escherichia coli by using the pBluescript SK+ and pUC18 vectors. By using the E. coli dnaK gene as a probe and by in vivo chromosome walking, three positive clones harboring the recombinant plasmids pKG1, pKG2, and pKG3 containing 1.2-kbp HindIII, 3.55-kbp EcoRV, and 1.2-kbp PstI fragments of the chromosome of C. acetobutylicum, respectively, were isolated. The cloned fragments partially overlapped, and together they spanned 4,083 bp of the clostridial genome that were completely sequenced. On one strand, four open reading frames of which the last was obviously truncated were identified. The last three genes showed high homology to the grpE, dnaK, and dnaJ heat shock genes of E. coli, respectively. They were preceded by an open reading frame (orfA) without any homology to sequences available in the EMBL or GenBank data bases. Typical translational start sites could be found in front of all four genes. Northern (RNA) blot analysis revealed transcripts of this region with a maximum length of 5.0 kb. Thus, these genes are probably organized in an operon. A transcription terminator could be found between the dnaK and dnaJ genes. By primer extension analysis, a major heat-inducible transcription start site was identified 49 bases upstream of orfA. This site was preceded by a region (5'-TTGACA[17 bp]TATTTT) that exhibited high homology to the consensus promoter sequences of gram-positive bacteria as well as sigma 70-dependent E. coli. Between this promoter and the initiation codon of orfA, a hairpin-loop structure with a possible regulatory role in the expression of these genes was found. Additional heat-inducible transcription start sites were located 69 bases upstream of orfA and 87 bases upstream of grpE; the corresponding promoter regions showed less similarity to other known promoter sequences. Maximum mRNA levels of this heat shock operon were found about 15 min after a heat shock from 30 to 42 degrees C. Our results indicate that orfA codes for an unknown heat shock protein.

Amino Acid Sequence↗

PubMed1992

Molecular characterization of the MalT-dependent periplasmic alpha-amylase of Escherichia coli encoded by malS.

malS, the gene encoding the periplasmic alpha-amylase, is under the regulatory control of the MalT protein, the gene activator of the Escherichia coli maltose system. We sequenced the DNA region encoding malS and its control elements. malS consists of an open reading frame of 2,028 base pairs encoding a protein of 676 amino acids with a deduced molecular weight of 75,664 including a typical amino-terminal signal sequence of 17 amino acids. The deduced amino acid sequence of malS was compared with that of other proteins. We found homologies to alpha-amylases and a cyclodextrin glucanotransferase but not to beta-amylases. In addition, MalS showed significant homology to another maltodextrin-utilizing and MalT-dependent enzyme of E. coli, maltodextrin glucosidase (MalZ) but not to amylomaltase (MalQ), the major maltodextrin-degrading enzyme. Conserved regions that have been proposed to constitute enzymatically active sites in alpha-amylases are present in MalS. Two of these sequences can also be found in the amino terminus of the lambda-receptor, a maltodextrin-specific channel in the outer membrane. The nucleotide sequence of the control region of malS revealed MalT binding sites correctly spaced for the start of the malS transcript. At the position 219 base pairs upstream of malS, we found a divergently transcribed gene, bax, which has been recognized previously. Downstream of malS, after a 513-base pair intergenic region, lies the convergently transcribed gene avtA, which codes for the alanine/valine transaminase.

Amino Acid Sequence↗

PubMed1994

A light-repressed transcript found in Synechococcus PCC 7002 is similar to a chloroplast-specific small subunit ribosomal protein and to a transcription modulator protein associated with sigma 54.

The gene encoding a novel light-repressed transcript (lrtA) contained within a 2.7-kbp EcoRI fragment has been cloned and sequenced from the unicellular cyanobacterium, Synechococcus PCC 7002. Northern analysis indicates that this transcript is synthesized rapidly in the dark, but upon 20 min of illumination, transcript levels fall below detectable limits. An open reading frame was located 378 bases from the start of the transcript which encodes a 21-kDa protein with significant homology to two hitherto different proteins. The protein sequence LrtA showed 37% sequence identity and 58% sequence similarity to the chloroplast-specific small subunit ribosomal protein, S30, and 37% sequence identity and 60% sequence identity and 60% sequence similarity to the reported transcription modulator protein of sigma 54 found in Klebsiella pneumonia and Azotobacter vinelandii. Expression of the lrtA gene product is not detectable within 1 h after placing the cells in the dark, however, within 2.5 min of illumination, [35S]methionine incorporated into a 21-kDa protein. To a lessor extent, [35S]methionine incorporation into a 17- and a 14-kDa protein was also seen which was followed by two other recognizable waves of translation at 5 and 10 min. This incorporation was not blocked by rifampicin added to dark-adapted cells prior to illumination. [35S]Methionine pulsed-labeling experiments suggested that the translation of lrtA occurred only during the first 10 min of reillumination of dark-adapted cells. The loss of initial [35S]methionine labeling in the light of the 21-kDa protein in a kanamycin-interrupted lrtA gene mutant suggests that the lrtA codes for the 21-kDa protein.

Amino Acid Sequence↗

PubMed2005

[Sequencing and expression analysis of a novel HMW-glutenin gene Kx from Crithopsis delileana].

Using SDS-PAGE analysis, the High-molecular-weight (HMW) glutenin subunits of two Crithopsis delileana accessions were detected. It was found that the two accessions had the same HMW glutenin subunits. Only one HMW glutenin subunit with the similar electrophoresis mobility to the y-type HMW glutenin subunit of hexaploid wheat was observed in C. delileana. However, It was indicated that this glutenin subunit was an x-type glutenin subunit Kx by gene sequence analysis. The full coding region of Kx gene is 2052bp and could encodes a mature protein with 661 amino acid residues. The Kx gene could be expressed in the bacterial expression system, and the expressed protein had the same electrophoresis mobility as that in the seed of C. delileana. The primary structure of Kx subunit was very similar to the x-type HMW glutenin subunits encoded by the A, B and D genomes of wheat, the C and U genomes of Aegilops, and the R genome of Secale cereale. In the phylogenetic analysis, Kx subunit was clustered together with Ax1 subunit by an interior parallelled branch. In conclsion, Kx gene is a novel x type glutenin subunit gene from C. delileana.

Amino Acid Sequence↗

PubMed1986

Nucleotide sequence of rat preputial gland beta-glucuronidase cDNA and in vitro insertion of its encoded polypeptide into microsomal membranes.

We have selected the rat preputial gland beta-glucuronidase as a model protein to study the sorting of newly synthesized lysosomal hydrolases to the lysosome. The complete coding sequence of beta-glucuronidase messenger RNA was determined from the sequences of a group of overlapping cDNA clones isolated from preputial gland cDNA libraries. The beta-glucuronidase mRNA primary translation product contains 648 amino acids, including an amino-terminal signal sequence of 22 residues. The polypeptide has four potential sites for the addition of asparagine-linked core oligosaccharides. A 376-residue segment of beta-glucuronidase shows extensive homology (23% sequence identity) to a portion of Escherichia coli beta-galactosidase. This homology most likely reflects an evolutionary relationship between the bacterial and eukaryotic enzymes and the conservation of structural features necessary for the glycosidase activity of both proteins. Translation of mRNA synthesized in vitro by transcription of a cDNA containing the entire beta-glucuronidase coding region yielded a polypeptide that was immunoprecipitated with anti-beta-glucuronidase antiserum and had the same electrophoretic mobility as the primary translation product of natural beta-glucuronidase mRNA. In the presence of microsomal membranes, the in vitro-synthesized beta-glucuronidase underwent cotranslational incorporation into the microsomes, as indicated by removal of the signal sequence and the addition of several oligosaccharide chains. The beta-glucuronidase cDNA will provide a useful tool to study the mechanism of mannose phosphorylation and other aspects of the sorting of lysosomal enzymes to lysosomes.

Animals↗

PubMed1987

[Expression in Escherichia coli cells of the nucleotide sequence of DNA coding for the bovine lipotropic hormone].

A cDNA fragment of bovine proopiomelanocortin coding for beta-lipotropic hormone was joined with a promoter and ribosome binding site of B. amyloliquefaciens and cloned in E. coli in pBR 327 plasmid. The level of beta-lipotropin synthesis in bacterial cells transformed by the obtained plasmid was estimated immunochemically. The level of beta-lipotropin production was shown to be 5 mg per liter of bacterial culture.

Amino Acid Sequence↗

PubMed1990

The IFN-gamma response of the murine invariant chain gene is mediated by a complex enhancer that includes several MHC class II consensus elements.

IFN-gamma induces the expression of the MHC class II-associated invariant chain (IN) protein in a variety of cells of nonlymphoid origin. Here we analyze the transcription from the murine invariant chain gene and delimit the cis-acting sequences which confer IFN-gamma responsiveness in human fibroblasts. The major start of transcription of the gene is located 29 bp 3' of a TATA box and 85 bp 5' of the single ATG codon which opens the reading frame. To identify the regulatory elements of the murine IN promoter which respond to IFN-gamma, the 5' flanking region of the gene including its capsite and 85 bp of coding region have been cloned in front of the bacterial chloramphenicol acetyl transferase (CAT) gene. Examination of this construct and various 5' and 3' deletion mutants for IFN-gamma inducibility in transient transfection assays revealed that DNA sequences between -261 and -189 were essential and sufficient for the induction. Removal of sequences between -215 and -189 reduced inducibility of the IN-promoter and abolished the capacity of the element to transmit inducibility to a heterologous promoter. Single or multiple base changes in other parts of the element also abolished inducibility. Cotransfection of a 350 molar excess of the IFN-gamma response element with an inducible IN-CAT chimeric construct blocked inducibility, suggesting positive regulation. A protein binding to the central part of the IFN-gamma response element was detectable in gel retardation experiments; it was active only in extracts from IFN-gamma-treated cells.

Animals↗

PubMed1989

Characterization of yeast mitochondrial RNase P: an intact RNA subunit is not essential for activity in vitro.

We have previously described a mitochondrial activity that removes 5' leaders from yeast mitochondrial precursor tRNAs and suggested that it is a mitochondrial RNase P. Here we demonstrate that the cleavage reaction results in a 5' phosphate on the tRNA product and thus the activity is analogous to that of other RNase Ps. A mitochondrial gene called the tRNA synthesis locus encodes an A + U-rich RNA required for this activity in vivo. Two regions of this RNA display sequence similarity to conserved sequences in bacterial RNase P RNAs. This sequence similarity coupled with the analogous activities of the enzymes has led us to conclude that the RNAs are homologous and that the tRNA synthesis locus does code for the mitochondrial RNase P RNA subunit. The smallest and most abundant transcript of the tRNA synthesis locus is 490 nucleotides long. However, during purification of the holoenzyme, RNA is degraded and pieces of the original RNA are sufficient to support RNase P activity in vitro.

Bacillus subtilis↗