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PubMed2004

Strain diversity and conserved genome elements in Strawberry mild yellow edge virus.

The complete nucleotide sequence of Strawberry mild yellow edge virus isolate D74, and the sequences of a 878 nt region of the coat protein and flanking regions of twenty three isolates of SMYEV were obtained and analysed. The full sequence of the aphid transmissible strain D74 was deduced and found to have an 86% sequence identity to the non-transmissible Agrobacterium infectious MY18 strain. In contrast to isolate MY18 the 5' terminal nucleotides (GAAAAC) of D74 are typical of those from other potexviruses. However, both MY18 and D74 have a non-AUG initiation codon for ORF2 encoding the triple gene block protein 1 (TGB1), and an overlapping TGB3 and coat protein (CP), features unique in the Potexvirus genus. Other conserved features of the genome, including stem-loop structures in the untranslated regions, and motifs common to related viruses are described. The previously postulated ORF6 of MY18 is absent in twenty of the isolates sequenced, including D74. Phylogenetic analysis places all isolates in one of three distinct groups/strains named here I (type-D74), II (type-9Redland), and III (type-MY18), with the majority of isolates, including all European isolates tested, belonging to strain I (type-D74).

Amino Acid Motifs↗

PubMed1998

Characterization of the UL16 gene product of herpes simplex virus type 2.

We have raised rabbit polyclonal antisera against a His-tagged herpes simplex virus type 1 (HSV-1) UL16 fusion protein, one of which very specifically reacted with 40 kDa and 41 kDa proteins in the lysates of HSV-1 and HSV-2-infected cells, respectively. Since its reactivity to the 41 kDa protein was clearly eliminated by pre-adsorption with E. coli lysates expressing the UL16 fusion protein, the antiserum was used to characterize the UL16 products of HSV-2. The HSV-2 UL16 protein was produced at the late phase of infection in a manner highly dependent on viral DNA synthesis and was distributed in both the nuclei and the cytoplasma of infected cells. In immunofluorescence studies, the UL16-specific fluorescence in the nuclei was shown to be detected as small discrete granules. On the other hand, the cytoplasmic fluorescence was diffusely distributed around the nucleus at 8 h postinfection but, at later times of infection, it was mainly detected as a mass at a perinuclear region. The analysis on its association with capsids has revealed that the UL16 protein copurified with C capsids but not B and A capsids, and that the association with C capsids was not tight. Moreover, our experiments have shown that a detectable level of the UL16 protein was not associated with extracellular virions, and that the partially purified UL16 proteins had a DNA-binding activity. These observations are consistent with the hypothesis that the UL16 protein plays a role in capsid maturation including DNA packaging/cleavage. We have also determined the complete nucleotide sequence of the HSV-2 UL16 gene and found that a nonstandard initiation codon may be used for its translation.

Amino Acid Sequence↗

PubMed2005

Molecular cloning and structural characterization of the functional human thymosin beta4 gene.

Thymosin beta4 (Tbeta4), the actin-sequestering protein that regulates the polymerization and depolymerization of actins, is widely distributed in animal tissues. Expression of this gene in human cells is developmentally regulated and appears to play critical roles in tumorigenesis. As a first step toward analyzing the transcriptional regulation of human Tbeta4 (hTbeta4), we isolated the gene encoding this peptide and characterized its structure features. Human Tbeta4 gene comprises three exons and two introns distributed over 2 kb with its transcription start site at 72 bp upstream of the initiation codon. Expression of the chloramphenicol acetyltransferase (CAT) reporter constructs directed by various parts of the 5'-flanking region of this gene was evaluated by transient transfection assays using human colorectal carcinoma SW480 cells as hosts. Significant promoter activity was found in the -437 to +29 region of hTbeta4 gene even though it lacks both TATA and CCAAT boxes. However, cis-element(s) responsible for PMA-induced expression of Tbeta4 gene was not identified within its 1.5-kb 5'-flanking region. Taken together, our data provide crucial information for further dissection of the molecular mechanism(s) underlying aberrant expression of the Tbeta4 gene during malignant progression of human cancers.

5' Flanking Region↗

PubMed1994

Analysis of the promoter of the human prostatic acid phosphatase gene.

From the analysis of two overlapping cosmid clones prepared from human genomic DNA libraries, a contig of 44 kb containing a 5' portion of the PAP gene and 17 kb of the upstream region was established. It was characterized by restriction mapping and sequence analysis of 2.5 kb upstream of the initiation codon. Two major transcription initiation sites were found to be located around 56 and 91 bp upstream of the initiation codon, as determined by nuclease S1 and primer extension mapping. Expression of the PAP gene was measured by Northern blots in the androgen responsive LNCaP cell line. It was found to be induced 2-3-fold by the addition of the synthetic androgen mibolerone to the cells. The induced mRNA levels were approx. 10-times lower than those for the prostate-specific antigen (PSA) in LNCaP cells.

Acid Phosphatase↗

PubMed2004

Promoter characterization of the mouse melanin-concentrating hormone receptor 1.

The gene encoding the mouse melanin-concentrating hormone receptor 1 was isolated and its structural organization and flanking regions were characterized. The 3' flanking region is marked by the presence of two polyadenylation signals but used with different frequencies. RNase protection and 5' rapid amplification of cDNA ends (RACE) identified multiple transcription initiation sites between -150 and -203 bp upstream of the ATG initiation codon. Functional analysis of deletion mutants reveals a cell independent transcriptional activity localized between nucleotide -305 and -589. The proximal 1.5 kb region does not possess consensus TATA or CAAT boxes but has several consensus sequences for regulatory elements including USF, GATA, AP1, AP4, MyoD, GKLF and Ikaros that could explain the broad expression of the receptor.

3' Flanking Region↗

PubMed2005

Identification of a novel Wee1 isoform.

We have identified a novel isoform of Wee1 kinase (Wee1i), which uses Met215 of Wee1 as its initiation codon. RT-PCR, Western blot, and in situ hybridization verified wee1i expression in mammalian cells, rat brain, and rat thymus. Recombinant and partially purified Wee1i from rat thymus displayed kinase activity comparable to or higher than Wee1. The N-terminal 214 residues of Wee1 facilitate its ubiquitin-dependent degradation to trigger mitotic entry. Since Wee1i, lack of these 214 residues, it may evade this degradation and thus provide constitutive Wee1-like kinase activity to inhibit mitotic cell proliferation. Thus, Wee1i may play an important role in differentiation and in tumor suppression.

Animals↗

PubMed2006

Identification of a novel, highly variable amino-terminal amino acid sequence element in the nuclear intermediate filament protein lamin B(2) from higher vertebrates.

By comparing newly available cDNA sequences of the human intermediate filament protein lamin B(2) with published sequences, we have identified an additional translation initiation codon 60 nucleotides upstream of the previously assumed translation start. In addition, corresponding sequences were identified in the chimpanzee, mouse, rat and bovine genes and cDNAs, respectively. Therefore, we generated antibodies against these potential 20 new amino acids of the human sequence. By immunoblot analysis and immunofluorescence microscopy we show that human lamin B(2) is indeed synthesized as a longer version than previously reported, because it contains these additional 20 amino acids. Notably, the sequence homology to mouse, rat and bovine lamin B(2) is significantly lower in this segment than in that between the second methionine codon and the start of the alpha-helical rod indicating that the tip of the "head" is engaged in more species-specific functions. Forced expression of the GFP-tagged authentic "long" and the 20 amino acid shorter version of lamin B(2) in human cultured SW-13 cells demonstrated that both the longer and the shorter version are properly integrated into the nuclear lamina, although the shorter version exhibited a tendency to disturb envelope architecture at higher expression levels.

Amino Acid Sequence↗

PubMed2004

RNA interactions in the 5' region of the HIV-1 genome.

The untranslated leader of the dimeric HIV-1 RNA genome is folded into a complex structure that plays multiple and essential roles in the viral replication cycle. Here, we have investigated secondary and tertiary structural elements within the 5' 744 nucleotides of the HIV-1 genome using a combination of bioinformatics, enzymatic probing, native gel electrophoresis, and UV-crosslinking experiments. We used a recently developed RNA folding algorithm (Pfold) to predict the common secondary structure of an alignment of 20 divergent HIV-1 sequences. Combining this analysis with biochemical data, we present a secondary structure model for the entire 744 nucleotide fragment, which incorporates previously recognized and novel structural elements. In particular, our data provided strong evidence for a long-distance interaction between the region encompassing the AUG Gag initiation codon and an upstream region and we demonstrate that this feature is highly conserved in distantly related human and animal retroviruses. To obtain information about tertiary interactions we applied an intramolecular UV-crosslinking strategy and identified a novel tertiary interaction within the PBS hairpin structure.

Algorithms↗

PubMed2000

A novel mutation of desert hedgehog in a patient with 46,XY partial gonadal dysgenesis accompanied by minifascicular neuropathy.

We describe a patient with 46,XY partial gonadal dysgenesis (PGD) who presented with polyneuropathy. Sural nerve pathology revealed peculiar findings characterized by extensive minifascicular formation within the endoneurium and with a decreased density of myelinated fibers. We found, in the patient, a homozygous missense mutation (ATG-->ACG) at the initiating codon in exon 1 of the desert hedgehog (DHH) gene, which predicts a failure of translation of the gene. The same heterozygous mutation was found in the patient's father. This is the first report of a human DHH gene mutation, and the findings demonstrate that mutation of the DHH gene may cause 46, XY PGD associated with minifascicular neuropathy.

Animals↗

PubMed2002

Non-AUG translation initiation of mRNA encoding plastid-targeted phage-type RNA polymerase in Nicotiana sylvestris.

A third nuclear gene encoding a bacteriophage T7-type RNA polymerase, NsRpoT-C, was isolated and characterized from Nicotiana sylvestris. The gene, NsRpoT-C, consists of 21 exons and 20 introns and encodes a polypeptide of 977 amino acid residues. The predicted NsRpoT-C protein shows the highest identity (72% amino acid identity) with Arabidopsis thaliana RpoT;3 which is a plastid-targeted protein. Surprisingly, comparison of the deduced amino acid sequence of NsRpoT-C with that of A. thaliana RpoT;3 predicted that the NsRpoT-C starts at a CUG triplet, a rare translation initiation codon. Transient expression assays in protoplasts from tobacco leaves demonstrated that the putative N-terminal transit peptide of NsRpoT-C encodes a targeting signal directing the protein into chloroplasts. This strongly suggests that NsRpoT-C functions as an RNA polymerase transcribing plastid-encoded genes. We have designated this protein NsRpoTp.

Amino Acid Sequence↗

PubMed2001

Inhibition of the human chemokine receptor CXCR4 by antisense phosphorothioate oligodeoxyribonucleotides.

The CXC chemokine receptor CXCR4/fusion, a major coreceptor for the T-cell line T-tropic (X4) HIV-1 virus, plays a critical role in T-tropic virus fusion and entry into permissive cells. In the present study, we describe the effects of an antisense phosphorothioate oligodeoxyribonucleotide (anti-S-ODN) on the inhibition of CXCR4 gene expression in X4 HIV-1 infected HeLa-CD4 cells, to find more efficacious therapeutic possibilities for human immunodeficiency virus type 1 (HIV-1) infection. The naked antisense phosphorothioate oligodeoxyribonucleotide (anti-S-ODN-1), containing the AUG initiation codon at the center of the oligodeoxyribonucleotide, showed a slightly higher inhibitory effect on HIV-1 gag p24 production among all sequences tested. We also examined the concomitant use of a basic peptide transfection reagent, nucleosomal histone proteins (RNP), for the delivery of the anti-S-ODN-1. The anti-S-ODN-1 encapsulated with RNP had higher inhibitory effects on p24 products than the naked anti-S-ODN-1. When the anti-S-ODN-1 encapsulated with RNP was incubated with HeLa-CD4 cells, the surface levels of this chemokine receptor showed high suppression, indicating sequence-specific inhibition. The activities of unmodified oligodeoxyribonucleotide are effectively enhanced by using a basic peptide, RNP.

CD4 Antigens↗

PubMed2000

Cloning and characterization of 5'-flanking region of mouse prostacyclin synthase gene.

To gain an insight into the mechanisms of prostacyclin expression, a genomic DNA clone harboring 2.0 kb of the 5'-flanking sequence of the mouse prostacyclin synthase (PGIS) gene was isolated. The 5'-flanking region did not possess a TATA box, but contained a GC-rich region and several consensus cis DNA elements. The major product of the primer extension analysis suggested that the transcription of the gene started from 72 bases upstream of the translational initiation codon. To analyze the PGIS promoter activity, the 2.0 kb fragment was fused to the luciferase gene and transient transfection assays were conducted with cultured rat vascular smooth muscle cells (VSMC). The fragment showed significant promoter activity in the cells. Analysis of a series of 5'-deletion constructs showed that the 5'-flanking regions spanning bases -371 to -285 and -229 to -119 were important for the basal transcriptional activity of the mouse PGIS gene. Gel mobility shift assays revealed that DNA-protein complexes were formed with the nuclear extracts from VSMC, and that the formation of these complexes was inhibited by excess consensus Sp1 oligonucleotide. Prior incubation of anti-Sp1 antibody with nuclear extracts in this assay resulted in supershift of the band for the DNA-protein complex. In addition, mutation of two Sp1 recognition motifs residing at bases -297 to -289 and -197 to -192 markedly reduced the basal PGIS promoter activity and retarded the band in a gel mobility shift assay. These results indicated that binding of one Sp1 to two Sp1 sites on the promoter region activated the basal transcription of the PGIS gene.

Animals↗

PubMed2003

Complete DNA sequence of the atp operon of the sodium-dependent F1Fo ATP synthase from Ilyobacter tartaricus and identification of the encoded subunits.

The atp operon of Ilyobacter tartaricus, strain DSM 2382, was completely sequenced using conventional and inverse polymerase chain reaction (i-PCR) techniques. It contains nine open reading frames that were attributed to eight structural genes of the F(1)F(o) ATP synthase and the atpI gene, which is not part of the enzyme complex. The initiation codons of all atp genes, except that of atpB coding for the a subunit, were identified by the corresponding N-terminal amino acid sequence. The hydrophobic a subunit was identified by MALDI mass spectrometry. The atp genes of I. tartaricus are arranged in one operon with the sequence atpIBEFHAGDC comprising 6,992 base pairs with a GC content of 38.1%. The F(1)F(o) ATP synthase of I. tartaricus has a calculated molecular mass of 510 kDa and includes 4,810 amino acids. The gene sequences and products reveal significant identities to atp genes of other Na(+)-translocating F(1)F(o) ATP synthases, especially in the F(o) subunits a and c which are directly involved in ion translocation.

Adenosine Triphosphate↗

PubMed1998

Identification of holocarboxylase synthetase (HCS) proteins in human placenta.

Holocarboxylase synthetase (HCS) is a key enzyme in biotin utilization in eukaryotic cells. In a previous work from our laboratory, we described the cloning and sequencing of a full-length human HCS cDNA. Due to the presence of three candidate sites for initiation of translation, the identification of full-length HCS proteins remains uncertain. Using antibodies directed against human HCS sequences, we have identified, in human placenta, three cytosolic HCS proteins, of 86, 82 and 76 kDa. Similar results were observed in lysates of cells transfected with an HCS expression vector, as well as with human HCS cDNA transcribed and translated in a cell-free system. When anti-HCS antibodies were tested for their ability to inhibit HCS enzymatic activity, only the antibody directed against a region of HCS from Ile128 to Pro398, and not the antibodies against more proximal N-terminal regions inhibited HCS activity, suggesting that the sequence from Ile128 to Pro398 is essential for the catalytic activity of this enzyme. HCS synthesized in a cell-free system was not translocated into rat liver mitochondria. These results suggest that our human HCS cDNA encodes the cytosolic forms of the enzyme. These results also suggest that mRNA encoding cytosolic HCS can be translated from all three translation initiation codons, Met1, Met7 and Met58.

Animals↗

PubMed2002

Characterization of mouse homolog of brain acyl-CoA hydrolase: molecular cloning and neuronal localization.

Acyl-CoA hydrolase could provide a mechanism via its potency to modulate cellular concentrations of acyl-CoAs for the regulation of various cellular events including fatty acid metabolism and gene expression. However, only limited evidence of this is available. To better understand the physiological role of this enzyme, we characterized a mouse brain acyl-CoA hydrolase, mBACH. The cloned cDNA for mBACH encoded a 338-amino-acid polypeptide with >95% identity to the human and rat homologs, indicating that the BACH gene is highly conserved among species. This was supported by the similarity in genomic organization of the BACH gene between humans and mice. Bacterially expressed mBACH was highly active against long-chain acyl-CoAs with a relatively broad specificity for chain length. While palmitoyl-CoA hydrolase activity was widely distributed in mouse tissues, it was marked in the brain, consistent with mBACH being almost exclusively distributed in this tissue, where >80% of the enzyme activity was explained by mBACH present in the cytosol. Immunohistochemistry demonstrated a neuronal localization of mBACH in both the central and peripheral nervous systems. In neurons, mBACH was distributed throughout the cell body and neurites. Although four isoforms except mBACH itself, that may be generated by the alternative use of exons of a single mBACH gene, were cloned, their mRNA levels in the brain were estimated to be negligible. However, a 50-kDa polypeptide besides the major one of 43-kDa seemed to be translated from the mBACH mRNA with differential in-frame ATG triplets used as the initiation codon. These findings will contribute to the functional analysis of the BACH gene using mice including genetic studies.

Alternative Splicing↗

PubMed1997

Cloning and characterization of the human mitochondrial 3-hydroxy-3-methylglutaryl CoA synthase gene.

We report the characterization of lambda and P1 phage clones containing the entire human mitochondrial 3-hydroxy-3-methylglutaryl CoA synthase (mHS) gene. The human mHS locus (HMGCS2) on chromosome 1p12-13 spans 25 kb and contains 10 exons. Exon 1 contains most of the mitochondrial leader, consistent with a recent hypothesis of the evolution of the ketogenic pathway. By primer extension and cDNA amplification (RACE-PCR) we localized the transcription start point (tsp) to 60 bp upstream of the initiation codon. Nine blocks of conserved sequence were identified by comparing the 5' flanking regions of the mHS genes of human and rat. The 5' flanking region contains potential binding sites for TATA-binding protein, Sp1, nuclear factor 1 (NF1), CAAT-box binding protein (C/EBP), hepatocyte nuclear factors 1 and 5 (HNF1, HNF5) and activator proteins 1 and 2 (AP1, AP2).

Animals↗

PubMed1998

Phosphorylation stabilizes alternatively spliced CD44 mRNA transcripts in breast cancer cells: inhibition by antisense complementary to casein kinase II mRNA.

CD44, the predominant vertebrate cell surface receptor for hyaluronan, exists in a variety of isoforms resulting from alternative splicing of a single gene. Particular spliced variants of CD44 correlate with increased cell motility, and with poor clinical prognosis in several kinds of carcinomas. Combinations of 9 variant exons that confer this enhanced motility on tumor cells are inserted into a single site in the middle of the extracellular domain of CD44. Evidence suggests that phosphorylation of 2 serine residues in the intracellular domain of CD44 are involved in controlling these events. However, evidence is lacking as to the nature of such kinases. Acidic amino acids in close proximity to these 2 serine residues suggests casein kinase II (CKII) is involved. We now show an antisense phosphorothioate oligonucleotide designed to hybridize to the AUG translation initiation codon of subunit CKII alpha' mRNA blocks in vivo phosphorylation of CD44 in MDA231 breast tumor cells, and at the protein level decreases ectopic expression of total CD44 as well as the metastatic v-7 CD44 isoform. Furthermore subplateau RT-PCR analysis demonstrated antisense transfected MDA231 tumor cells had significant down-regulated or eliminated mRNA transcripts of metastatic CD44 isoforms. CKII as a CD44-associated serine kinase therefore may serve as an important molecule in a signaling cascade that produces a variety of cellular responses in MDA231 breast cancer cells. Since the 3'-untranslated region of CD44 mRNA contain 4 dispersed AUUUA sequences which serve as signals targeting mRNA for rapid turnover, a mechanism is proposed by which CD44 phosphorylation mediates labile message stabilization, hence providing insights into the processes involved in cancer cell growth, invasion and metastasis.

Alternative Splicing↗

PubMed2000

The efficiency of different IRESs (internal ribosomes entry site) in monocistronic mRNAS.

The IRES from poliovirus and from encephalomyocarditis virus (EMCV) added between the cap and the AUG initiator codon were strong inhibitors of chloramphenicol acetyltransferase gene expression in three different cell types. The poliovirus IRES also inhibited bGH (bovine growth hormone) cDNA expression in the HC11 mammary cell line when added between the rabbit whey acidic gene promoter and the cDNA whereas the HTLV-1 IRES showed a stimulatory effect in the same situation. RNA stem loops were added before HTLV-1 (SUR) and the BiP (Immunoglobulin heavy-chain Binding Protein) IRESs followed by the firefly luciferase gene under the control of Rous sarcoma virus (RSV) promoter. The RNA loops abolished the expression of the reporter gene almost completely. These data suggest that the different IRESs may favour or inhibit translation of monocistronic mRNA.

5' Untranslated Regions↗