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PubMed2001

Molecular characterization of the genomic breakpoint junction in the t(11;18) (q21;q21) translocation of a gastric MALT lymphoma.

The t(11;18) translocation, fusing the API2 and MALT1 genes, is one of the most frequent chromosomal translocations associated with mucosa-associated lymphoid tissue (MALT) lymphomas. The translocation breakpoints have been cloned and characterized at the mRNA sequence level. Although the genomic organization of the API2 gene has been described, hitherto the genomic sequence of MALT1 remains unknown. To gain some insight into the mechanism that generates this translocation, we cloned and sequenced an API2-MALT1 fused transcript as well as genomic DNA of the t(11;18) translocation from a MALT lymphoma. We localized the API2 breakpoint within intron 7. Nucleotide sequence analysis revealed that the genomic breakpoint junction possesses the consensus heptamers of immunoglobulin V(D)J recombination signal sequences, all the matches being completely present on the API2 allele and five of seven matches on the MALT1 allele. These data suggest that the translocation in the MALT lymphoma might have been mediated in part by an aberrant V(D)J recombination event.

Base Sequence↗
PubMed1996

Immunological comparisons of integrin alpha IIb beta 3 (GPIIb-IIIa) expressed on platelets and human erythroleukemia cells: evidence for cell specific differences.

Platelet glycoprotein IIb-IIIa (GPIIb-IIIa, alpha IIb beta 3) is expressed on the cell surface of the human erythroleukemia (HEL) cell line. Previous studies have demonstrated differences in GPIIb-IIIa ligand binding properties of HEL cells when compared to platelets. Although the mRNA sequences for GPIIb and GPIIIa are identical in platelets and HEL cells, cell specific differences in the conformation states of the GPIIb-IIIa complex may exist and may explain in part the contrasting functional properties. Two monoclonal antibodies (mAbs), an anti-GPIIb mAb C3 and an anti-GPIIIa mAb D3, were used to determine whether differences in GPIIb-IIIa conformational states could be measured. Initial studies in a purified system showed that the mAbs' binding to isolated GPIIb-IIIa conformers was increased to the active GPIIb-IIIa and to dissociated receptor subunits when compared to the inactive form. Furthermore, soluble active GPIIb-IIIa was a much better inhibitor of D3 binding to the immobilized receptor compared to soluble inactive GPIIb-IIIa. Extending these studies with intact cells, we detected at least two classes of binding sites for each mAb on each cell type. Differences in Bmax and in the relative affinities of the mAbs were identified and may represent subpopulations of GPIIb-IIIa conformations. Total HEL cell and platelet GPIIb-IIIa was determined in our binding assays using a radiolabeled GPIIb-IIIa complex specific mAb, 10E5. HEL cells express approximately five times more GPIIb-IIIa on a per cell basis. The percent of total GPIIb-IIIa that represented each class of mAb binding sites was determined. In summary, the relative differences in GPIIb-IIIa conformation found on platelets and HEL cells may be related to cell-specific ligand binding properties and activation states of the receptor.

Analysis of Variance↗
PubMedDate not supplied

Complete characterization of the 3' region of the human and mouse hereditary hemochromatosis HFE gene and detection of novel splicing forms.

The human HFE gene was identified in 1996 as the gene whose mutations are responsible for hereditary hemochromatosis in most patients. Expression analysis by Northern blot indicated that the gene was approximately 4.1 kb in length. However, the cDNA reported was only 2716 bp. These results implied that at least 1.4 kb of the mRNA remained to be identified. In the present study, we detected several 3' EST clones while screening the genomic region of the gene in search of potential additional HFE mRNA sequences. Subsequent sequencing of these EST clones and RT-PCR experiments revealed that exon 7 of the HFE gene has, in fact, a length of 1944 bp and it presents two polyadenylation signals. The new human HFE exon 7 region has been screened in non-C282Y HH patients in search for new putative mutations. Mouse 3' RACE experiments also further extend the previously reported mouse HFE exon 6 sequence. Additionally, we report two novel end forms of the human HFE gene detected by 3' RACE experiments and several novel splicing forms identified in the HepG2 cell line.

3' Untranslated Regions↗
PubMed1998

Antisense nucleic acids targeted to the thymidylate synthase (TS) mRNA translation start site stimulate TS gene transcription.

Thymidylate synthase (TS) is a key enzyme in the synthesis of DNA and a target for cancer chemotherapeutic agents. Antisense TS nucleic acids may be useful in enhancing anticancer drug effectiveness. MCF-7 and HeLa cells were transfected with vectors expressing antisense TS RNA or with antisense oligodeoxynucleotides (AS-ODNs) to different TS mRNA regions. Antisense RNAs were targeted to 30 bases of the TS mRNA including part of the stem loop at the translation start site and to 30 bases spanning the exon1/exon2 boundary. AS-ODNs were targeted to the translation start site and the translation stop site. Antisense nucleic acids complementary to the translation start site (and not the exon1/exon2 boundary or translation stop site) significantly enhanced constitutive TS gene transcription. Therefore, TS mRNA sequences appear to be involved in a novel pathway controlling TS gene transcription. Induced transcription could hinder antisense-based attempts to inhibit TS and must be considered when designing such strategies.

Blotting, Northern↗
PubMed2001

A new protein expressed in bone marrow cells and osteoblasts with implication in osteoblast recruitment.

To study osteoblast recruitment from bone marrow cells, a rat femur cDNA library was screened by in situ hybridization for novel mRNA sequences that are frequently expressed in both marrow cells and osteoblasts. One isolated clone, called RP59, is described here. Northern blots indicated two bands of 2.6 and 2.8 kb in femur and spleen, tissues containing high amounts of immature mesenchymal cells, and no or little expression in other tissues. The cDNA sequence revealed a reading frame for a repetitive protein composed of arrays of 14-mers and phased phosphorylation sites. Antisera versus RP59 detected a single band of 90 kDa by Western blotting of femur extract. Immunohistochemistry indicated strong RP59 presence in the cytoplasm of bone marrow cells and weaker presence in nuclei of osteoblasts. Intermediate stages were found between strongly labeled, round, free bone marrow cells and weaker labeled, fibroblast-like young osteoblasts associated with bone matrix. These data indicated that marrow cells with high RP59 content were recruited into growing bone tissue. RP59 may help to study the transition of bone marrow cell to osteoblast in more detail.

Amino Acid Sequence↗
PubMed1995

Structure, localization, and molecular phylogeny of a GnRH cDNA from a paracanthopterygian fish, the plainfin midshipman (Porichthys notatus).

Multiple forms of gonadotropin releasing hormone (GnRH) are found within several species of teleost fishes. Within the infradivision Euteleostei, the superorder Paracanthopterygii represents one of the last major groups to be examined with respect to the GnRH mRNA sequence. The plainfin midshipman, Porichthys notatus, is a common member of this superorder which is intermediate between the ancestral euteleost taxa and the more derived Acanthopterygians (percomorphs). The goals of this study were to: (1) determine the cDNA sequence of prepro-GnRH in the plainfin midshipman, (2) address the anatomical localization of midshipman prepro-GnRH gene expression, and (3) perform a cladistic analysis using all currently known cDNA sequences of prepro-GnRH. We report 460 base pair of cDNA sequence containing the entire protein coding region, and 5'- and 3'-untranslated regions. The deduced amino acid sequence indicates that this cDNA encodes a GnRH decapeptide identical in sequence to that originally isolated in salmon (Trp7, leu8 - GnRH). Northern analysis demonstrated transcripts in brain, ovary, and testis (600-700 nucleotides). PCR showed that the ovarian prepro-GnRH was identical to that found in brain. In situ hybridization labeled neurons in the ganglion of the terminal nerve and the preoptic area, forebrain areas previously observed to contain GnRH-like immunoreactivity. Last, a phylogenetic analysis of 18 prepro-GnRH sequences grouped the Paracanthopterygii with the Acanthopterygii. However, this recent clade was distinct from two separate and more ancestral lineages, the Paracanthopterygii (salmonids) and Ostariophysi (represented by catfish).

Amino Acid Sequence↗
PubMed1998

The hyaluronidase gene HYAL1 maps to chromosome 3p21.2-p21.3 in human and 9F1-F2 in mouse, a conserved candidate tumor suppressor locus.

We recently cloned and expressed the major hyaluronidase activity from human plasma, HYAL1, and found that the protein is 40% identical to the testicular hyaluronidase, PH-20. The HYAL1 mRNA sequence was used in a homology search of the mouse database of expressed sequence tags (dbEST). Two ESTs were obtained and, in combination with 5'RACE-PCR, were used to clone the mouse HYAL1 ortholog (Hyal1). Hyal1 codes for a protein of 462 amino acids that is 73% identical to the human sequence. Hyal1 stably expressed in human embryonic kidney cells resulted in a 20,000-fold increase of hyaluronidase activity. Sequence-tagged sites derived from the HYAL1 gene from both species were used to isolate P1 genomic clones that were used as probes for fluorescence in situ hybridization. The human gene was localized to chromosome 3p21 and the mouse gene to a syntenic region on chromosome 9F1-F2. In mouse, serum hyaluronidase polymorphism has previously been mapped by an interspecific backcross to 60 cM from the centromere of chromosome 9, which corresponds to a cytogenetic location of 9F1-F2. The mouse Hyal1 gene is therefore very likely to be responsible for the hyaluronidase polymorphism linked to this locus. We also present evidence that human HYAL1 is identical to an uncharacterized gene positionally cloned by others from chromosome 3p21.3 that is homozygously deleted in several small-cell lung carcinoma cell lines.

Amino Acid Sequence↗
PubMed1999

The gene structure of the human growth factor bound protein GRB2.

The growth factor bound protein GRB2, a 25-kDa cytosolic protein, plays a key role in two separate pathways of the insulin signal transduction system leading from the insulin receptor to the Ras proteins and thus affecting mitogenic signaling. GRB2 regulates Ras activation through association with the guanine nucleotide exchange factor Sos. The GRB2/Sos complex can connect with insulin receptor substrate 1 (IRS-1), which is one of the primary targets of the insulin and insulin-like growth factor receptors. In a second pathway, independent of IRS-1, GRB2 links the insulin receptor to Ras signaling through another adapter protein, called Shc. In protooncogenic and other noninsulin signaling systems, GRB2 appears to link receptor tyrosine kinases to Ras in similar pathways as well. This study presents the exon-intron organization of the human GRB2 gene. After primers were placed across the known mRNA sequence, Long PCR products spanning introns and their adjacent splice sites were amplified and adequately sequenced to establish the splice sites and flanking regions. The gene was found to consist of five exons (ranging from 78 to 186 bp) and of four introns (from approximately 1 to approximately 7 kb). Intron primers for the respective exons were generated using the newly found flanking sequences. All exons were successfully amplified and sequenced, and the data obtained from Long PCR sequencing were confirmed.

Adaptor Proteins, Signal Transducing↗
PubMed1998

Specific correlations between relative synonymous codon usage and protein secondary structure.

We found significant species-specific correlations between the use of two synonymous codons and protein secondary structure units by comparing the three-dimensional structures of human and Escherichia coli proteins with their mRNA sequences. The correlations are not explained by codon-context, expression level, GC/AU content, or positional effects. The E. coli correlation is between Asn AAC and the C-terminal regions of beta-sheet segments; it may result from selection for translational accuracy, suggesting the hypothesis that downstream Asn residues are important for beta-sheet formation. The correlation in human proteins is between Asp GAU and the N termini of alpha-helices; it may be important for eukaryote-specific sequential, cotranslational folding. The kingdom-specific correlations may reflect kingdom-specific differences in translational mechanisms. The correlations may help identify residues that are important for secondary structure formation, be useful in secondary structure prediction algorithms, and have implications for recombinant gene expression.

Bacterial Proteins↗
PubMed2000

Inhibition of the RNA-dependent transactivation and replication of human immunodeficiency virus type 1 by a fluoroquinoline derivative K-37.

Human immunodeficiency virus type 1 (HIV-1) is unique in that it encodes its own transcriptional activator Tat, which specifically binds to the viral mRNA sequence TAR (transactivation response) element and activates viral transcription at the step of elongation as well as initiation. We recently reported that fluoroquinoline derivatives inhibited HIV-1 replication most likely by blocking viral transcription. In this report, we investigated the mechanism of action of one such compound 7-(3, 4-dehydro-4-phenyl-1-piperidinyl)-1, 4-dihydro-6-fluoro-1-methyl-8-trifluoromethyl-4-oxoquinoline-3-carbox ylic acid (K-37). We demonstrated that K-37 inhibited not only Tat but also other RNA-dependent transactivators. No effect was observed with DNA-dependent transactivators such as p65 (NF-kappaB) and Gal4VP16. Moreover, K-37 did not inhibit carboxyl-terminal domain (CTD)-kinase activities of CDK-activating kinase (CAK) and positive transcription elongation factor b (P-TEFb), which are known to be involved in Tat-mediated transactivation at the step of transcriptional elongation. It is suggested that RNA-mediated transactivation may involve a common unknown factor to which K-37 directly interacts. Since K-37 did not appear to block DNA-mediated transactivation and thus did not show strong nonspecific cytotoxicity as reported previously, K-37 and its derivative compounds are considered to be feasible candidates for a novel AIDS therapy.

Animals↗
PubMed1992

Detection of transcriptionally active hepatitis B virus DNA in peripheral mononuclear blood cells after infection during immunosuppressive chemotherapy using the polymerase chain reaction.

Using PCR we have studied mononuclear peripheral blood leucocytes (PMBLs) from HBV-infected immunosuppressed patients in order to detect the presence of HBV genomes. Our results indicate that non-transient PMBL infection is common in immunotolerant carriers. In addition, the presence of pregenomic mRNA sequences suggests that virus replication may take place in PMBLs, possibly implicating the latter as a source of virus after replication has ceased in the liver.

Adolescent↗
PubMed1984

Histone gene expression in human diploid fibroblasts: analysis of histone mRNA levels using cloned human histone genes.

The cellular abundance of H2A, H2B, H3 and H4 histone mRNA sequences was determined prior to and at various times after stimulation of non-dividing human diploid fibroblasts to proliferate. The representation of histone mRNAs was quantitated by electrophoretic fractionation of total cellular RNAs, diffusion transfer to nitrocellulose and hybridization with a series of cloned genomic human histone sequences. The levels of mRNAs for the four core histones were observed to be temporally and quantitatively coupled with both DNA replication and histone protein synthesis. Therefore, a contribution to the regulation of histone gene expression at a transcriptional level is suggested.

Cells, Cultured↗
PubMed1983

Androgen regulation of prostatic binding protein messenger RNA studied by using cloned complementary DNA.

The construction of a double-stranded cDNA library using rat prostatic poly(A)RNA and pBR322/kappa 1776 system and the isolation of three prostatic binding protein (PBP) cDNA clones are described. These cDNA clones were characterized and identified by in situ hybridization, mRNA selection-translation and immuno-precipitation as coding for the three subunit components, C1, C2, and C3, of PBP. These clones were used in hybridization experiments with prostatic poly(A)RNA to determine the effect of testosterone on the levels of PBP-mRNA. The results showed that synthesis of these mRNAs varied in response to either androgen withdrawal or replacement. Accumulation of PBP-mRNAs coding for C2 and C3 components occurred 1 hr after androgen administration to castrated rat, whereas the mRNA coding for the C1 component did not appear until 4 hr after androgen replacement. Quantitation of PBP-mRNA sequences in nuclear and polysomal poly(A)RNAs showed that they did not vary coordinately in response to androgen withdrawal. These results indicate differential regulation of PBP genes and suggest possible multiple levels of androgen control of PBP synthesis.

Animals↗
PubMed1993

A plant mitochondrial gene encodes a protein involved in cytochrome c biogenesis.

Analysis of a transcribed region in the mitochondrial genome of Oenothera revealed an open reading frame (ORF) of 577 codons (orf577) that is also conserved in carrot, here encoding a protein of 579 amino acids (orf579). RNA editing alters the mRNA sequence of orf577 in Oenothera with 46 C to U transitions, many of which improve sequence similarity with the homologous Marchantia gene orf509. The deduced polypeptides show significant similarity with the ccl1-encoded protein involved in cytochrome c biogenesis in the photosynthetic bacterium Rhodobacter capsulatus. A highly conserved domain is also found in plastid ORFs, suggesting that these bacterial, chloroplast and mitochondrial genes encode polypeptides with analogous functions in assembly and maturation of cytochromes c.

Amino Acid Sequence↗
PubMed1984

Developmental and nutritional regulation of the messenger RNAs for fatty acid synthase, malic enzyme and albumin in the livers of embryonic and newly-hatched chicks.

The mRNAs for fatty acid synthase and malic enzyme were almost undetectable in total RNA extracted from the livers of 16-day old chick embryos. Both mRNAs increased in abundance between the 16th day of incubation and the day of hatching. In neonates, fatty acid synthase mRNA level was dependent on nutritional status, increasing slowly if the chicks were starved and rapidly if they were fed. The abundance of malic enzyme mRNA decreased in starved neonatal chicks and increased in fed ones. When neonates were first fed and then starved, starvation caused a large decrease in the abundance of both mRNAs. Conversely, feeding, after a period of starvation, resulted in a substantial increase in both mRNAs. The relative abundances of fatty acid synthase and malic enzyme mRNAs correlated positively with relative rates of enzyme synthesis. Thus, nutritional and hormonal regulation of the synthesis of these two 'lipogenic' enzymes is exerted primarily at a pre-translational level. The abundance of albumin mRNA decreased significantly between the 16th day of incubation and the day of hatching but did not change thereafter in fed or starved chicks. The relative stability of albumin mRNA levels after hatching attests to the selectivity of the nutritional regulation of fatty acid synthase and malic enzyme mRNAs. The decrease in albumin mRNA which occurred between 16 days of incubation and hatching contrasts with the increase in albumin mRNA sequences which occurred during late gestation in the fetal rat (20). High levels of albumin in the chick embryo may be related to the lack of an analogue of mammalian alpha-fetoprotein in birds.

Animals↗
PubMed1990

The genetic code in mitochondria and chloroplasts.

The universal genetic code is used without changes in chloroplasts and in mitochondria of green plants. Non-plant mitochondria use codes that include changes from the universal code. Chloroplasts use 31 anticodons in translating the code; a number smaller than that used by bacteria, because chloroplasts have eliminated 10 CNN anticodons that are found in bacteria. Green plant mitochondria (mt) obtain some tRNAs from the cytosol, and genes for some other tRNAs have been acquired from chloroplast DNA. The code in non-plant mt differs from the universal code in the following usages found in various organisms: UGA for Trp, AUA for Met, AGR for Ser and stop, AAA for Asn, CUN for Thr, and possibly UAA for Tyr. CGN codons are not used by Torulopsis yeast mt. Non-plant mt, e.g. in vertebrates, may use a minimum of 22 anticodons for complete translation of mRNA sequences. The following possible causes are regarded as contributing to changes in the non-plant mt: directional mutation pressure, genomic economization, changes in charging specificity of tRNAs, loss of release factor RF2, changes in RF1, changes in anticodons, loss of lysidine-forming enzyme system, and disappearance of codons from coding sequences.

Animal Population Groups↗
PubMed1988

Evolution of chorion structural genes and regulatory mechanisms in two wild silkmoths: a preliminary analysis.

We report a preliminary analysis of structural and regulatory evolution of the A and B chorion gene families in two wild silkmoths, Antheraea pernyi and Antheraea polyphemus. Homospecific and heterospecific dot hybridizations were performed between previously characterized A. polyphemus complementary DNA clones and total or stage-specific follicular mRNAs from the two species. The hybridization patterns indicated substantial interspecies changes in the abundance of corresponding mRNA sequences (heteroposic evolution) without substantial changes in their developmental specificities (heterochronic evolution). In addition, the proteins encoded in the two species by corresponding mRNAs were determined by hybrid-selected translation followed by electrophoretic analysis. The results suggested that the proteins evolve in size, presumably through internal deletions and duplications.

Animals↗