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Biomedical subjects

J Choe

Publications and source records attributed to J Choe.

At least 55 records · Page 3Linked to original sources

RNA helicase activity of Escherichia coli SecA protein.

SecA protein of Escherichia coli (E. coli), an ATPase essential for the translocation of precursor proteins, was found to have an additional activity of RNA helicase. This RNA unwinding activity of SecA was tested with two kinds of RNA duplex with different predicted stability. Each of these duplexes is consisted of two strands of unequal length with single-stranded ends. The RNA helicase activity of SecA required ATP and divalent cations. Confirmation of this activity came from the inhibition of unwinding of the RNA duplex when SecA was preincubated with its own polyclonal antibody. The biological significance of the RNA helicase activity of E. coli SecA protein is discussed.

Adenosine Triphosphatases↗

An in-line suturing device to simplify sacrospinous vaginal vault suspension.

A disposable suturing instrument is used in our surgical method for sacrospinous vault suspension to facilitate suture placement and retrieval. The pararectal space is dissected and the suturing device is placed just medial to the lateral third of the sacrospinous ligament-coccygeus muscle complex. Depression of the device's firing button advances a standard needle in a controlled circular path through the sacrospinous ligament-coccygeus muscle complex. The needle is retrieved with a straight-needle holder at a consistent location, 3 mm from the shaft of the instrument. A second suture is placed 0.5-1 cm medial to the first suture. If the holding strength for either suture is considered inadequate, the device is reloaded with the same suture and subsequent bites are taken. The procedure is completed using standard methods. In ten women treated for vaginal vault eversion, lateral dissection was completed in less than 10 minutes, and passage of two sutures through the sacrospinous ligament was accomplished in less than 2 minutes. There were no complications. One patient described mild buttock pain that resolved in 1 week. At 4-6 months' follow-up, vaginal examination with maximal straining demonstrated direct apposition of the vaginal wall to the sacrospinous ligament.

Female↗

Identification of cis-regulatory elements in the upstream regulatory region of human papillomavirus type 59.

Human papillomavirus type 59 (HPV-59) was cloned from a vulvar intraepithelial neoplasia and the complete nucleotide sequence was determined. This virus is closely related to HPV-18 and -39 (60% homology in nucleotide sequence) and is grouped with the genital HPV types. In the present paper, we demonstrate that the HPV-59 E2 transactivator represses its E6 promoter-mediated transcription. We have also analyzed cis-regulatory elements in the upstream regulatory region (URR) of HPV-59 using chloramphenicol acetyl transferase assays as well as electrophoresis mobility shift assays (EMSA). The results allow for a subdivision of the HPV-59 URR into three regions of activity: distal (nt 7149-7493), central (nt 7493-7742), and proximal (nt 7742-7748). In particular, the 250 bp (nt 7493-7742) of the central region plays an important role as a constitutive enhancer element for the maximal transcription of the E6 promoter. Our results suggest that the transcription factors AP1, Oct1, SP1 and unidentified factors bind to the HPV-59 E6 promoter region, whereas NF1, GRE and TFIID fail to bind despite the presence of putative binding sites in the DNA sequence.

DNA-Binding Proteins↗

Identification of sequence requirement for the origin of DNA replication in human papillomavirus type 18.

DNA replication of human papillomavirus type 18 is dependent on viral proteins E1 and E2 and the subsequent interaction of these proteins with the viral origin of replication. Using a site-directed mutagenesis analysis, we examined the sequence requirement for the DNA replication of the human papillomavirus type 18. We showed that both the E1BS palindrome and E2BS are the major determinants of the HPV replication efficiency. In particular, abolishing E2 binding sites demonstrated that E2BS makes a significant contribution towards HPV-18 DNA replication. Each part of the 18-bp inverted repeat sequence of the E1BS motif showed a clear functional difference between two regions: nt 13-21 (3' half segment) is evidently more important for replication than nt 4-12 (5' half segment). Besides E1BS and E2BS, cis-acting elements such as the poly-A6 track, perhaps the YY1 binding site, and the TATA box sequence within the origin region exhibited some contributions to optimum replication. In addition, inserting an enhancer region to the minimum origin DNA derivatives increased replication approximately 2-fold compared with the wild type levels and showed some compensational effects on loss of the cis-element within the HPV-18 minimum origin, suggesting that an enhancer region is required for efficient replication of the papillomavirus origin. These results suggest that the formation of an E1-E2-ori complex is important for replication, and other sequences near the E1 and E2 binding sites assist E1-E2-ori-mediated DNA replication in vivo.

Base Sequence↗

Towards defining a minimal functional domain for NTPase and RNA helicase activities of the hepatitis C virus NS3 protein.

Hepatitis C virus (HCV) possesses two separate enzymatic functions in the NS3 protein: a protease and an NTPase/RNA helicase. In order to determine the minimal domain for NTPase and RNA helicase activities of the HCV NS3 protein, serial deletion mutants were constructed. The NS3H protein a fusion protein of 25 amino acids (aa) from an expression vector and the C-terminal 466 aa of the HCV NS3 protein, contains an NTPase/RNA helicase activity. We made deletion mutants of 10, 30, 50, 97, and 135 aa from the C-terminus and 16 and 32 aa from the N-terminus of the NS3H protein. The deleted protein lacking 50 aa from the C-terminus still possessed both activities, while the protein lacking 97 aa from the C-terminus lost an RNA helicase activity. The mutant lacking 16 amino acids from the N-terminus retained the enzymatic activities and the N-terminal 32 aa deleted mutant lost an NTPase/RNA helicase activity. A combinational deletion mutant lacking 16 aa the N-terminus and 50 aa from the C-terminus retained the enzymatic activities. These results show that the functional domain of the HCV NTPase/ RNA helicase is about 400 aa in length and maps between NS3 residues 1209 and 1608.

Acid Anhydride Hydrolases↗

Mutational analysis of the hepatitis C virus RNA helicase.

The carboxyl-terminal three-fourths of the hepatitis C virus (HCV) NS3 protein has been shown to possess an RNA helicase activity, typical of members of the DEAD box family of RNA helicases. In addition, the NS3 protein contains four amino acid motifs conserved in DEAD box proteins. In order to inspect the roles of individual amino acid residues in the four conserved motifs (AXXXXGKS, DECH, TAT, and QRRGRTGR) of the NS3 protein, mutational analysis was used in this study. Thirteen mutant proteins were constructed, and their biochemical activities were examined. Lys1235 in the AXXXXGKS motif was important for basal nucleoside triphosphatase (NTPase) activity in the absence of polynucleotide cofactor. A serine in the X position of the DEXH motif disrupted the NTPase and RNA helicase activities. Alanine substitution at His1318 of the DEXH motif made the protein possess high NTPase activity. In addition, we now report inhibition of NTPase activity of NS3 by polynucleotide cofactor. Gln1486 was indispensable for the enzyme activity, and this residue represents a distinguishing feature between DEAD box and DEXH proteins. There are four Arg residues in the QRRGRTGR motif of the HCV NS3 protein, and the second, Arg1488, was important for RNA binding and enzyme activity, even though it is less well conserved than other Arg residues. Arg1490 and Arg1493 were essential for the enzymatic activity. As the various enzymatic activities were altered by mutation, the enzyme characteristics were also changed.

Adenosine Triphosphatases↗

Up-regulation of Bcl-xL expression protects CD40-activated human B cells from Fas-mediated apoptosis.

CD40--CD40L interactions between resting B cells and activated T cells are essential for germinal center formation. It has been shown that CD40L can induce both Fas expression and susceptibility to Fas-mediated killing in B cells, while anti-Ig can partially rescue B cells from Fas-mediated killing. However, the intracellular mechanism for this phenomenon is not known. We examined the expression of Fas and bcl-2 family gene products, such as Bcl-2, Bcl-x, Bax, and Mcl-1, in human tonsillar B cells. The activation of naive B cells by CD40L induced transient expression of Bcl-xL. As the Bcl-xL level decreased in CD40-activated B cells, the cells became susceptible to apoptosis by anti-Fas antibodies. Though anti-Ig did not change the Fas expression, it protected CD40-activated B cells from Fas-mediated killing by up-regulating Bcl-xL expression. The addition of anti-Ig did not significantly change Bcl-2, Bax, and Mcl-1 levels compared to those of B cells activated by CD40L alone.

Apoptosis↗

Characterization of RNA binding activity and RNA helicase activity of the hepatitis C virus NS3 protein.

The Hepatitis C Virus (HCV) NS3 protein has RNA binding activity, RNA-stimulated NTPase activity, and RNA helicase activity. The RNA binding activity of the C-terminal domain of the HCV NS3 protein is less sensitive to pH, KCl, and MgCl2 than NTPase and the RNA helicase activity. The overall order of the binding of homoribopolymer for the NS3 protein was poly(U) > > poly(A) > poly(G), poly(C). The minimal RNA binding size of the HCV NS3 protein was determined using a gel retardation assay and is estimated between 7 nt and 20 nt. The HCV RNA helicase unwinds RNA/DNA heteroduplexes as well as RNA/RNA duplexes and it catalytically translocates in the 3' to 5' direction.

Base Sequence↗

Cellular and molecular factors that regulate the differentiation and apoptosis of germinal center B cells. Anti-Ig down-regulates Fas expression of CD40 ligand-stimulated germinal center B cells and inhibits Fas-mediated apoptosis.

To investigate the molecular and cellular mechanisms underlying the selection, differentiation, and apoptosis of germinal center (GC) B cells, we have established a culture system containing a follicular dendritic cell (FDC) line, HK. The mAb, 3C8, which is specific to HK cells and recognizes dendritic network in the GC, was developed and provided additional evidence that HK cells are related to FDC by sharing a unique surface Ag. The roles for CD40 ligand (CD40L) and T cell-derived cytokines in the differentiation of GC B cells were investigated in our culture system. We show that there are two distinct stages of GC B cell differentiation. In the early stage, GC B cells undergo spontaneous apoptosis unless they are stimulated by CD40L. In the secondary stage, IL-10 directs GC B cell differentiation toward the generation of plasma cells, while the absence of IL-10 stimulation leads to the generation of memory B cells. The major function of CD40L was found in the enhancement of cell recovery and the augmentation of memory B cell generation. Although GC B cells are Fas+, GC B cells are at first resistant to, but then become sensitive to, anti-Fas killing after 24 h in culture with CD40L, which coincides with the gradual increase in Fas expression on GC B cells. Furthermore, anti-Ig down-regulated Fas expression on CD40L-stimulated GC B cells, suggesting that Ag receptor engagement down-regulates Fas expression and prevents Fas-mediated apoptosis of GC B cells. Our data imply that GC T cells have an important role in the differentiation and apoptosis of GC B cells. GC T cells expressing both CD40L and Fas ligand have a dual function on GC B cells, helper or killer, depending on the status of target B cells. In the early stage, GC T cells stimulate the extensive proliferation of GC B cells, ensuring a large repertoire of B cells for selection. In the later stage, GC T cells kill B cells via Fas-Fas ligand interactions unless GC B cells are positively selected by Ags present on FDC.

ADP-ribosyl Cyclase↗

Transforming activities of human papillomavirus type 59 E5, E6 and E7 open reading frames in mouse C127 cells.

The DNA sequence from a human papillomavirus type 59 (HPV 59) has been recently determined. The HPV 59 genome consists of 7896 nucleotides (nt). A comparative analysis of this sequence with the sequences of other HPVs revealed the closest homology to HPV 18 (71%). To test the transforming activities of HPV 59 DNA and its gene products, several plasmids expressing HPV 59 open reading frames (ORF) were constructed. The E5, E6, and E7 ORFs of HPV 59 were inserted into pRc/CMV vector containing a promoter of cytomegalovirus to test the transforming activities of these ORFs. When these DNAs were transfected into mouse C127 cells, all three ORFs were independently able to transform C127 cells in the presence of G418, although the full length HPV 59 DNAs failed to induce the focus-formation. The E7 ORF showed the strongest transforming activity and the E5 ORF exhibited the weakest transforming activity. Cell lines transformed by E5, E6, and E7 ORFs were established and they grew anchorage-independently. The presence of HPV 59 ORF DNA was confirmed by polymerase chain reaction (PCR) and Southern blot analysis in HPV 59 ORFs-transformed cell lines.

Animals↗

Topogenic effect of positively charged N-terminal amino acid in ER translocation of yeast alpha-factor precursor.

Expression of fusion proteins between prepro-alpha-factor and somatostatin (SRIF) in yeast, resulted in the correct processing and secretion of the heterologous 14-amino acid SRIF peptide (1). When the chimeric genes were placed under the control of yeast acid phosphatase (PHO5) promoter, significant amount of an unglycosylated form of the fusion precursor molecule accumulated intracellularly, suggesting disruption of an endoplasmic reticulum-mediated function. We report here that the appearance of the precursor is due to an alteration in the three amino terminal residues of the chimera, i.e., Met-Arg-Phe in native prepro-alpha-factor is changed to Met-Phe-Lys in the hybrids. The unglycosylated precursor represents a population of molecules that are disrupted at an early stage of targeting to or translocation across the endoplasmic reticulum membrane. Our data demonstrate that the N-terminus plays an important role in topogenesis. Furthermore, these results show that translocation and glycosylation can be uncoupled from protein synthesis in vivo, and therefore can be posttranslational events in yeast.

Amino Acids↗

C-terminal domain of the hepatitis C virus NS3 protein contains an RNA helicase activity.

The Hepatitis C Virus (HCV) NS3 protein contains amino acid motifs of a serine proteinase, a nucleotide triphosphatase (NTPase), and an RNA helicase based on amino acid sequence analysis. Proteinase and NTPase activities of the HCV NS3 protein were reported by several investigators. Here, we show that the recombinant HCV NS3 protein purified from a T7 promoter and His-tag expression system possesses an RNA helicase activity. The recombinant HCV NS3 protein consists of 466 amino acids from the carboxy terminal of a HCV NS3 open reading frame and 25 additional residues from the vector. The recombinant HCV NS3 protein was purified by metal-binding chromatography. The helicase activity requires ATP and divalent cations such as Mg2+ and Mn2+. The helicase activity was abolished by monoclonal antibody specific to the HCV NS3 protein.

Adenosine Triphosphate↗

Characterization of uvi15+, a stress-inducible gene from Schizosaccharomyces pombe.

The uvi15+ gene of Schizosaccharomyces pombe is a member of a group of stress-inducible genes transcription levels of which increase in response to DNA-damaging agents or heat shock. It encodes a polypeptide of calculated molecular mass 11641 Da, with no significant sequence similarity to other known heat shock proteins. The steady-state level of the uvi15+ gene product of about 12 kDa was increased by heat shock and canavanine, an amino acid analog. This gene also showed a transient increase in expression as cells moved into diauxic shift phase. Although deletion of the uvi15+ gene did not affect the mitotic growth or thermotolerance of cells, the mutant cells rapidly lost viability in stationary phase and under starvation conditions. These cells also showed a defect in sporulation ability. These results suggest that the uvi15+ gene encodes a stress response protein involved in the maintenance of cell viability during entry into stationary phase or under starvation conditions.

Amino Acid Sequence↗

Transfection of a differentiated human hepatoma cell line (Huh7) with in vitro-transcribed hepatitis C virus (HCV) RNA and establishment of a long-term culture persistently infected with HCV.

T7 RNA polymerase transcripts of a putative full-length cDNA clone of hepatitis C virus type 1 (HCV-1) were used to transfect a differentiated human hepatoma cell line, Huh7. The transfected genome replicated in cells, as evidenced by the appearance of progeny HCV RNA, detection of negative-strand viral RNA, and incorporation of [3H]uridine into the viral genome. Incubation of naive Huh7 cells with conditioned medium from transfected cells resulted in a new HCV infection, suggesting the production of biologically active virus in the inoculum. Maintenance of the transfected cells under serum-free culture conditions resulted in the selection of persistently infected cells which displayed a distinctive cellular morphology. This is the first demonstration that HCV RNA produced from cloned HCV cDNA is infectious and replication competent. This approach should provide a valuable system for studying HCV replication, persistence, and pathogenicity.

Base Sequence↗

Genomic structure of c-Ki-ras proto-oncogene of the hermaphroditic fish Rivulus marmoratus (teleostei: Rivulidae).

The ras homologue of the rivulid fish Rivulus marmoratus was isolated and characterized by screening about 3.0 x 10(5) genomic clones from a Rivulus genomic library using human c-Ha-ras probe. When this clone was partially sequenced focusing on the region coding exons, it showed 97.5% amino acid homology to the human c-Ki-ras gene. The Rivulus c-Ki-ras gene spans about 6.3 kb and consists of five exons including the alternative splicing exon 4a/4b. The exon-intron boundaries of Rivulus c-Ki-ras gene coincided with the GT/AG rule of consensus splice acceptor and donor sequences as in mammalian c-Ki-ras genes. Amino acid sequence analysis of some domain regions of the Rivulus c-Ki-ras gene revealed 100% identity to mammalian c-Ki-ras gene. This report is the first that elucidate the entire structure of c-Ki-ras in a fish.

Animals↗

Nucleotide sequence and phylogenetic classification of human papillomavirus type 59.

The complete nucleotide sequence of the HPV 59 DNA genome, isolated from a vulvar intraepithelial neoplasia, was determined. It consists of 7896 nucleotides. A comparative analysis of this sequence with the sequences of other HPV types revealed the closest homology to HPV 18 (71%), HPV 45 (70%), and HPV 39 (69%). Phylogenetic analysis of the complete L1 ORFs of HPV 59 and other papillomaviruses exclusively groups all HPVs which have been detected in mucosal lesions into one major branch. This major branch, in turn, includes two specific subgroups containing all high risk viruses associated with malignant mucosal lesions. The motif in the L2 ORF thr-thr-pro-ala-val/ile-leu/ile-asp/asn-val/ile, an extension of a previously reported mucosal motif, is highly conserved in all HPV types detected in mucosal lesions, whereas it is totally absent in those viruses exclusively associated with cutaneous lesions.

Amino Acid Sequence↗

The human retinoblastoma susceptibility gene promoter is positively autoregulated by its own product.

The product of the retinoblastoma susceptibility gene is a 105-kDa protein that has properties of a cell cycle regulatory factor. Previous reports indicated that two distinct DNA-binding factors, RBF-1 and ATF, play an important part in the transcription of the human retinoblastoma gene (Rb). Recently, we demonstrated that pRb activates expression of the human transforming growth factor-beta 2 gene through ATF-2. Since the human Rb gene promoter also contains an ATF-2-like binding site, we examined whether pRb can regulate its own expression through ATF-2. Here we report that overexpression of Rb stimulates Rb promoter activity through the ATF binding site in a variety of different cell types. Mutation of the ATF binding site of the Rb promoter abolishes the Rb autoinduction. We have also determined that the carboxyl-terminal domain of pRb is responsible for the Rb autoinduction through ATF-2. Rb autoinduction may be important for maintaining the action of pRb during cell growth, and loss of autoinductibility may contribute to retinoblastoma.

Activating Transcription Factors↗

Absence of the intron-D-exon of c-Ha-ras oncogene in the hermaphroditic fish Rivulus marmoratus (Teleostei: Rivulidae).

We have cloned ras genes from the hermaphroditic fish Rivulus marmoratus genomic library by screening about 3.0 x 10(5) genomic clones. When one out of 19 ras genomic clones was sequenced, it showed 95.8% amino acid homology to the human c-Ha-ras gene and was named the Rivulus c-Ha-ras gene. The Rivulus c-Ha-ras gene spanned about 3.7 kb and consisted of four exons encoding 189 amino acids. The exon-intron boundaries also coincided with the rule of GT/AG of consensus splice acceptor and donor sequences. The Rivulus c-Ha-ras gene does not, however, have the intron-D-exon (IDX) that has been reported to exist between the third and the fourth exon of the mammalian c-Ha-ras genes, and which is involved in negative control of p21 c-Ha-ras expression and transforming activity of this gene. This is the first report on the structure of the fish c-Ha-ras gene.

Amino Acid Sequence↗