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PubMed2005

tmRNA and associated ligands: a puzzling relationship.

Translation is an efficient and accurate mechanism, needing thorough systems of control-quality to ensure the correspondence between the information carried by the messenger RNA (mRNA) and the newly synthesized protein. Among them, trans-translation ensures delivering of stalled ribosomes when translation occurs on truncated mRNAs in bacteria, followed by the degradation of the incomplete nascent proteins. This process requires transfer-messenger RNA (tmRNA), an original molecule acting as both a tRNA and an mRNA. tmRNA first enters the decoding site of stuck ribosomes and, despite the lack of any codon-anticodon interaction, acts as a tRNA by transferring its alanine to the incomplete protein. Translation then switches to a small internal coding sequence (mRNA domain), which encodes a tag directing the incomplete protein towards degradation. Although playing a central role during trans-translation, tmRNA function depends on associated proteins. Genetic, biochemical and recent structural data are starting to unravel how the process takes place, by involving three main protein partners. Small protein B (SmpB) interacts with the tRNA-like domain (TLD) of tmRNA and is indispensable and specific to the process. Elongation factor Tu (EF-Tu) binds simultaneously the TLD and brings aminoacylated tmRNA to the ribosome, as for canonical tRNAs. Ribosomal protein S1 forms complexes with tmRNA, facilitating its recruitment by the stalled ribosomes. The chronology of events, however, is poorly understood and recent data shed light on the functions attributed to the proteins involved in trans-translation. This review focuses on the puzzling relationship that tmRNA has with these three protein ligands, putting forward trans-translation as a highly dynamical process.

Ligands↗
PubMed1987

Localization of brain angiotensinogen mRNA by hybridization histochemistry.

The topographical distribution of rat brain angiotensinogen (Ao) mRNA was determined using hybridization histochemistry (in situ hybridization) with two different hybridization probes, a 32P-labelled 42 residue oligonucleotide and a full-length complementary (antisense) RNA labelled with either sulfur 35 or phosphorus 32. Low levels of Ao mRNA sequences were detected throughout the brain while high levels were restricted to specific areas often corresponding to classical nuclear boundaries. All areas in which angiotensin II-like immunoreactivity had been previously detected contained moderate to high levels of Ao mRNA and many previously undetected areas were also found to contain high levels of this mRNA. The results underline the ubiquitous presence of angiotensinogen-synthesizing cells in the brain and support previous evidence that the angiotensinogen gene could be expressed by several types of brain cells.

Angiotensinogen↗
PubMed1984

The influence of glucocorticoid on the fibrinogen messenger RNA content of rat liver in vivo and in hepatocyte suspension culture.

The plasma concentration of fibrinogen, one of the major acute-phase proteins produced by the liver, increases during the acute-phase response as a result of enhanced synthesis in liver. Since adrenal-cortical hormones have been thought to have a key role in the regulation of the fibrinogen synthesis, fibrinogen-polypeptide mRNA sequences were determined in the present study, by using a specific complementary-DNA probe, in RNA fractions obtained from rat hepatocytes exposed to glucocorticoids in vitro (hepatocyte suspension cultures) and in vivo. Maximal induction of the fibrinogen-polypeptide mRNA (to 400% of the control value) was found in vitro at 0.1 microM-dexamethasone after 9 h of incubation. The same magnitude of induction was obtained with 20 microM-cortisol or 60 microM-corticosterone. In contrast with the findings in vitro, no induction of the fibrinogen-polypeptide mRNA was observed in the liver at various times after injection of different doses of glucocorticoids into rats. These results suggest that more complex regulatory mechanisms are involved and that glucocorticoids are not the sole regulatory factors in vivo in the enhanced synthesis of fibrinogen during the acute-phase response.

Animals↗
PubMed1990

Two forms of the basic fibroblast growth factor receptor-like mRNA are expressed in the developing mouse brain.

The embryonic neuroepithelium gives rise to the components of the central nervous system in the mature animal. To study the early development of the murine central nervous system we have sought to isolate growth factor receptors from the neuroepithelium of the neural tube of 10-day-old mouse embryos. Because many growth factor receptors are members of the protein-tyrosine kinase family, we have used the polymerase chain reaction to amplify mRNA sequences from 10-day-old mouse embryo neuroepithelium; these sequences lie between the nucleotide sequences of two highly conserved amino acid motifs from the catalytic domain of protein-tyrosine kinases. By using this technique we have isolated a clone encoding the murine basic fibroblast growth factor receptor (bFGF-R), as well as a shorter form of this mRNA. This latter cDNA comprised 75% of the bFGF-R cDNA clones isolated from the immortalized neuroepithelial cell lines. This variant mRNA, designated here as N-bFGF-R, appears to be expressed at higher levels in neuronal cells in early stages of development. The bFGF-R is a member of a multigene family, as demonstrated by Southern blot analysis and the cloning of two other members of this family.

Amino Acid Sequence↗
PubMed1991

The use of antisense oligodeoxynucleotides (aODNs) for the therapy of cancer.

Although specific cancer targets are difficult to identify, the recent development of antisense oligodeoxynucleotides (aODNs) as inhibitors of gene expression has been shown to provide a new and useful tool in antiblastic management. aODNs are able to specifically interact with gene or mRNA sequences and inhibit the expression of relevant molecules for cancer pathogenesis and progression. Since alpha-DNA polymerase (pol-alpha) plays an essential role in cell proliferation, aODNs to pol-alpha have been synthesized in order to block mRNA translation and affect the growth of MDA-MB 231, human breast cancer cell line and SW626 ovarian cancer cells. A rapid colorimetric test (MTT assay) which measures cell growth and survival has been employed to evaluate the effects induced by ODN treatment. The present experimental results demonstrate that the aODNs to pol-alpha are able to significantly affect cell proliferation. This study provides an encouraging basis for the exploitation of ODNs as therapeutic agents in vitro and in future clinical application.

Cell Division↗
PubMed1992

Epstein-Barr virus latent gene expression in uncultured peripheral blood lymphocytes.

In this study of Epstein-Barr virus (EBV) latency, the polymerase chain reaction was used in modified form for amplification and detection of viral mRNA sequences in peripheral blood lymphocytes from healthy seropositive adults. Six known promoters for latent gene expression and eight known gene products were identified in in vitro-immortalized lymphocytes and in the cell lines established spontaneously from seropositive adults. We examined whether mRNA expression in uncultured B cells from four seropositive adults was the same as that which occurred in spontaneously established EBV-positive B-cell lines from the same individuals. A minimum of 17 polymerase chain reaction targets was required to circumscribe the known latent mRNA structures. Expression of the C promoter for the EBNA genes was detected in B-cell RNA from three of the four subjects. Transcripts initiated from the alternative W promoter for EBNA expression were not detected. The spliced transcripts detected in the B cells contained only the C2-to-W1 alternative splice, which was nonproductive for EBNA4 gene expression. None of the other EBNA open reading frames were detected spliced onto the 3' ends of the C promoter-initiated RNAs. Spliced RNA from the TP gene was detected in all four subjects. Expression of the TP gene was restricted to TP1 promoter-initiated RNAs, as no TP2 promoter-initiated transcripts were detected. Expression of RNA from the LMP gene was not detected. The F promoter which is active in the restricted expression latency that occurs in Burkitt's lymphoma cells was not detected being expressed in peripheral blood B cells. This pattern of latent gene expression is unique to uncultured B cells, indicating that there are profound differences between viral latent states in vitro and in situ and suggesting a central role for the TP gene in the latency of EBV.

Adult↗
PubMed2005

Characterization of equine intestinal fatty acid binding protein and its use in managing horses with colic.

OBJECTIVE: To determine the nucleotide sequence of the equine intestinal fatty acid binding protein (I-FABP) gene, its expression in various regions of the gastrointestinal tract, and the use of measuring I-FABP in horses with colic. Animals-86 horses with colic. PROCEDURE: The mRNA sequence for the I-FABP gene was obtained by use of a rapid amplification of complementary DNA ends technique. Comparative I-FABP gene expression was quantitated by use of a real-time reverse transcription-polymerase chain reaction assay. Amounts of I-FABP in abdominal fluid and plasma were measured by use of an ELISA kit. Association between I-FABP concentrations and clinical variables was performed by nonparametric analysis, and associations of these variables with intestinal ischemia were determined by the Spearman correlation test. RESULTS: The nucleotide sequence had 87% identity with human I-FABP The I-FABP gene was highly expressed in the small intestinal mucosa but had low expression in the colon. High concentrations of I-FABP in abdominal fluid correlated with an increase in protein concentrations in peritoneal fluid and nonsurvival, whereas plasma I-FABP concentrations correlated with the necessity for abdominal surgery. Clinical variables associated with intestinal ischemia included the color and protein content of abdominal fluid and serum creatine kinase activity. CONCLUSIONS AND CLINICAL RELEVANCE: Determination of I-FABP concentrations in abdominal fluid and plasma may be useful for predicting survival and the need for abdominal surgical intervention in horses with colic. Furthermore, serum creatine kinase activity and color and protein concentrations of abdominal fluid may be useful in the diagnosis of intestinal ischemia.

Animals↗
PubMed1993

Insulin-like growth factor-I (IGF-I) antisense oligodeoxynucleotide mediated inhibition of DNA synthesis by WI-38 cells: evidence for autocrine actions of IGF-I.

Insulin-like growth factor-I (IGF-I) is elaborated into culture medium by WI-38 cells, a human embryonic lung fibroblast cell line, and may participate in the autocrine stimulation of DNA synthesis. We have confirmed the expression of IGF-I by these cells and documented that they express the type 1 IGF receptor and a number of IGF-binding proteins. In situ hybridization histochemistry demonstrated relatively uniform expression of IGF-I and type 1 IGF receptor transcripts among WI-38 cells. To determine whether WI-38-synthesized IGF-I exerted mitogenic effects, a 15-base oligodeoxynucleotide complementary to the 5'IGF-I mRNA sequence (IGF-I AS-Oligo), including the translation start site, was incubated with cultured cells in an attempt to inhibit IGF-I synthesis. The IGF-I AS-Oligo was stable in cell culture, formed intracellular duplexes with IGF-I mRNA, and at 2 microM reduced IGF-I in conditioned medium by 83%. The IGF-I AS-Oligo also inhibited [3H]thymidine incorporation into DNA in a dose-dependent fashion (by 77% at 2 microM and by 95% at 20 microM). This reduction in DNA synthesis was prevented when the medium was supplemented with 100 ng/ml IGF-I. The oligomer also decreased the abundance of IGF-binding proteins in conditioned medium. The IGF-I AS-Oligo appears to exert its effects by blocking IGF-I mRNA translation, rather than blocking transcription or initiating RNase-H activity, because the abundance of IGF-I transcripts was not decreased in its presence. These findings confirm an essential role for IGF-I in WI-38 cell DNA synthesis and are consistent with autocrine actions by WI-38 cell IGF-I.

Base Sequence↗
PubMed1989

In situ hybridization demonstration of poly-adenylated RNA sequences in formalin-fixed paraffin sections using a biotinylated oligonucleotide poly d(T) probe.

An in situ hybridization technique has been developed for assessing poly(A)+ RNA preservation in routine pathology specimens. The method detects poly-adenylated RNA sequences in tissue sections using a biotinylated polydeoxythymidine (poly d(T)) probe. The probe was prepared from single-stranded 25-30 base oligo d(T) and was biotinylated using the enzyme terminal deoxynucleotide transferase with biotin-11-dUTP and dTTP in the ratio 1:4. The hybridization protocol uses varying concentrations of proteinase K to unmask mRNA sequences and the biotin-labelled hybrids are demonstrated after hybridization under standard conditions by the application of streptavidin and biotinylated alkaline phosphatase. Alkaline phosphatase was visualized using a Fast Red naphthol-capture method and the sections were counterstained with haematoxylin. The results have confirmed that the method is specific for poly(A)+ RNA and shows that poly(A)+ RNA can be demonstrated in routine formalin-fixed sections using non-radioactive techniques with retention of morphology. It also provides a means of optimizing the hybridization conditions for specific mRNA probes and produces a staining pattern demonstrating the relative level of poly(A)+ RNA per cell which may reveal new information about cell activity and tissue function.

Base Sequence↗
PubMed1990

Variable region sequences of pathogenic anti-mouse red blood cell autoantibodies from autoimmune NZB mice.

New Zealand Black (NZB) mice spontaneously develop a severe autoimmune hemolytic anemia due to the production of anti-mouse red blood cell (MRBC) autoantibodies. The contribution of variable region genes and somatic mutations in the pathogenicity of anti-MRBC autoantibodies was investigated by mRNA sequencing of eight NZB anti-MRBC monoclonal autoantibodies, among which five are capable of inducing anemia in BALB/c mice. Here we report that at least three VH gene families (J558, J606 and 3609) and five Vchi subgroups (V chi 8, 9, 19, 21 and 28), in combination with several D, JH and Jchi gene segments, encode anti-MRBC autoantibodies. Thus, the NZB anti-MRBC autoantibodies, whether pathogenic or not, are encoded by a large number of immunoglobulin gene elements and by members of known VH and Vchi gene families with preferential usage of VH gene families most distal to the D regions. The presence of several mutations in the JH gene segments of both IgM and IgG anti-MRBC autoantibodies, whether pathogenic or not, strongly suggests that their VH regions may be highly mutated and that the mechanism of somatic diversification might be important in the generation of anti-MRBC autoantibodies. Our results support the idea that anti-MRBC autoimmune responses are likely to be generated by an antigen-driven mechanism.

Amino Acid Sequence↗
PubMed1986

The human albumin gene. Characterization of the 5' and 3' flanking regions and the polymorphic gene transcripts.

We have characterized the 5' and 3' regions of the human albumin gene with respect to nucleotide sequences, mRNA transcription initiation and polyadenylation. There are at least two transcription initiation sites and two polyadenylation sites in the human albumin gene. The multiple transcription initiation sites are utilized almost equally. The two polyadenylation sites are used differentially, with the site proximal to the protein termination codon dominating. The "TATA" and the "CCAAT" boxes are present at about 30 and 90 nucleotides upstream of the putative cap sites. About 250 nucleotides immediately 5' to the transcription initiation sites are highly conserved among the human, rat, and chicken. Within the 1-kilobase pair 5' flanking region of the human albumin gene there are 8- and 35-base pair alternating purine/pyrimidine sequences, primarily consisting of dG and dT, and three nucleotide segments exhibiting homology to the proposed progesterone receptor-binding site. In these and other characteristics, the 5' flanking region of the human albumin gene is distinct from the corresponding region of the human alpha-fetoprotein gene. Each of the two polyadenylation sites of the human albumin gene is preceded by a AATAAA hexamer. In addition, the first polyadenylation site has several conserved sequences believed to play a role in the 3'-end formation. The second polyadenylation site lacks these signals which may explain why it is used less frequently. In spite of these differences the two polyadenylation sites show a high overall sequence similarity, suggesting that they arose by duplication. There is no major difference between the normal liver and hepatoma cells in the relative utilization of multiple sites for transcriptional initiation and polyadenylation of the human albumin gene, suggesting that the albumin mRNA polymorphism has no direct relevance to hepatocarcinogenesis.

Albumins↗
PubMed1988

Organization and differential expression of two highly similar genes in the rabbit alcohol-inducible cytochrome P-450 subfamily.

The exon-intron organization of two rabbit genes that hybridize with cytochrome P-450 3a (P-450ALC) cDNA has been determined by restriction mapping and sequence analysis. Gene 1 encodes cytochrome P-450 3a as judged by the complete identity of its coding nucleotide sequence with P-450 3a cDNA. Gene 2 encodes a previously uncharacterized cytochrome P-450 that is 97% identical in primary structure to P-450 3a, with 16 amino acid differences scattered throughout the protein. Genes 1 and 2, which are 10 and 9 kilobases in length, respectively, are comprised of 9 exons with exon-intron junctions occurring at identical positions along the mRNA sequences. Each gene contains two transcription start sites approximately 27 and 33 nucleotides upstream from the translation initiation codon, as determined by primer extension and S1 nuclease protection experiments. The predicted lengths of gene 1 and 2 transcripts from the first transcription start site to the poly(A) attachment site are 1999 and 1660 nucleotides, respectively. This difference in size is primarily the result of a 338-base pair deletion in the 3' nontranslated portion of the gene 2 transcript relative to that of gene 1. The two genes show considerable similarity in their 5' flanking regions, including a "TATAA" transcriptional promoter element at position -28. However, a 32-base pair element that is repeated in gene 1 is present only as a single inexact copy in gene 2. By use of synthetic oligonucleotides as hybridization probes, gene 2 transcripts were shown to be present in poly(A)+ RNA from untreated rabbit liver at approximately 50% of P-450 3a mRNA levels. In kidney, however, no gene 2 mRNA was detected although 3a mRNA was present at approximately 10% of the level in liver.

Amino Acid Sequence↗
PubMed1998

The genomic organization of NKG2C, E, F, and D receptor genes in the human natural killer gene complex.

Interactions of natural killer cell receptors with their cognate ligands play a major role in regulating NK cell function. The NKG2 gene family encodes several highly similar proteins, which are known to form heterodimers with the CD94 receptor. These dimers play a role in the inhibition as well as the activation of NK cells. We have analyzed the gene structures of the NKG2C, D, E, and F genes, and determined their genomic organization. Restriction mapping and sequencing revealed the four genes to be closely linked to one another, and of the same transcriptional orientation. An exon duplication within the NKG2C and E genes was identified, although the duplicated version of this exon has not yet been found in mRNA sequences. The NKG2C, E, and F genes, despite being highly similar, are variable at their 3' ends. We show that NKG2C consists of six exons, whereas NKG2E has seven, and the splice acceptor site for the seventh exon occurs in an Alu repeat. NKG2F consists of only four exons and part of exon IV is in some cases spliced to the 5' end of the NKG2D transcript. NKG2D has only a low similarity to the other NKG2 genes.

Base Sequence↗
PubMed2006

Synthesis of branched antisense oligonucleotides having multiple specificities. Treatment of hormone insensitive prostate cancer.

Antisense oligonucleotides (oligos) directed against transforming growth factor-alpha (TGF-alpha) and its binding site, the epidermal growth factor receptor (EGFR), have demonstrated in vitro and in vivo efficacy against both the PC-3 and LNCaP prostate tumor models. In an attempt to increase the efficiency of these oligos a new type of antisense compound called a bispecific oligo has been evaluated in vitro both alone and in combination with traditional chemotherapeutic agents. These bispecifics, which were first proposed in this journal in 2004, include binding sites for both TGF-alpha and EGFR along the same stretch of complementary DNA. Such bispecifics are able to deliver essentially two antisense activities in an equal molar ratio and can be directed against mRNA encoding proteins of different biochemical pathways. The first bispecifics were developed against two proteins regulating a single autocrine loop. Subsequent bispecifics have been developed which target both EGFR and the apoptosis regulating protein bcl-2. Bispecific activity of a single linear sequence oligo has already been shown to have efficacy. To further develop this multispecific approach, we now propose a branched antisense compound, again, having multiple binding site activities (to complementary sequenced mRNA). Active oligos would be attached to a fat soluble backbone which might enhance targeting and also intracellular entry, release and activity. Such a structure would also permit the customization of these branched forms to include oligos targeting specific proteins related to the growth of various tumor types. Problems associated with the development of antisense oligos have included both membrane solubility and specific targeting. By designing this branched form of antisense structure, multiple activities can be retained (added), solubility improved and delivery enhanced. Such a new formulation would include several antisense oligos covalently bound to and branching off from a lipid-like backbone. An elongated hydrocarbon chain would increase fat solubility and would permit oligo incorporation into nanoparticles or liposome derived delivery vehicles. Specific delivery of oligos could also be enhanced by the tendency of these nanoparticle or liposomal microbubbles to be disrupted under the influence of ultrasonic waves beamed at the targeted tissue.

Cell Line, Tumor↗
PubMed1985

The complete sequence of the chicken alpha-cardiac actin gene: a highly conserved vertebrate gene.

We sequenced the entire chicken alpha-cardiac actin gene. A single intron was positioned 20 bp upstream from the initiation ATG codon in the 5' non-coding region while the coding region was interrupted by 5 introns at amino acid positions 41/42, 150, 204, 267, and 327/328. Sequencing allowed the first comparison of the alpha-cardiac and alpha-skeletal actin transcriptional promoters. These highly G+C rich promoters share two regions of homology which are found at position -134 (10 bp) and -296 (12 bp) in the alpha-cardiac actin promoter. A smaller 9 bp motif (CCGCGCCGG) homologous to the -134 sequence was detected before, between and after the TATA and CAAT boxes of the alpha-cardiac actin gene. The polyadenylation signal (AATAAA) was located 156 bp downstream from the translation termination codon. The complete length of the alpha-cardiac actin mRNA excluding the poly A tail is 1370 nucleotides. The 3' noncoding transcribed portion of the chicken alpha-cardiac actin gene was found to be extraordinarily conserved when compared to the human and rat alpha-cardiac actin mRNA sequences.

Actins↗
PubMed2003

Transcript identification by analysis of short sequence tags--influence of tag length, restriction site and transcript database.

There exist a number of gene expression profiling techniques that utilize restriction enzymes for generation of short expressed sequence tags. We have studied how the choice of restriction enzyme influences various characteristics of tags generated in an experiment. We have also investigated various aspects of in silico transcript identification that these profiling methods rely on. First, analysis of 14 248 mRNA sequences derived from the RefSeq transcript database showed that 1-30% of the sequences lack a given restriction enzyme recognition site. Moreover, 1-5% of the transcripts have recognition sites located less than 10 bases from the poly(A) tail. The uniqueness of 10 bp tags lies in the range 90-95%, which increases only slightly with longer tags, due to the existence of closely related transcripts. Furthermore, 3-30% of upstream 10 bp tags are identical to 3' tags, introducing a risk of misclassification if upstream tags are present in a sample. Second, we found that a sequence length of 16-17 bp, including the recognition site, is sufficient for unique transcript identification by BLAST based sequence alignment to the UniGene Human non-redundant database. Third, we constructed a tag-to-gene mapping for UniGene and compared it to an existing mapping database. The mappings agreed to 79-83%, where the selection of representative sequences in the UniGene clusters is the main cause of the disagreement. The results of this study may serve to improve the interpretation of sequence-based expression studies and the design of hybridization arrays, by identifying short tags that have a high reliability and separating them from tags that carry an inherent ambiguity in their capacity to discriminate between genes. To this end, supplementary information in the form of a web companion to this paper is located at http:// biobase.biotech.kth.se/tagseq.

Algorithms↗
PubMed2006

TACT: Transcriptome Auto-annotation Conducting Tool of H-InvDB.

Transcriptome Auto-annotation Conducting Tool (TACT) is a newly developed web-based automated tool for conducting functional annotation of transcripts by the integration of sequence similarity searches and functional motif predictions. We developed the TACT system by integrating two kinds of similarity searches, FASTY and BLASTX, against protein sequence databases, UniProtKB (Swiss-Prot/TrEMBL) and RefSeq, and a unified motif prediction program, InterProScan, into the ORF-prediction pipeline originally designed for the 'H-Invitational' human transcriptome annotation project. This system successively applies these constituent programs to an mRNA sequence in order to predict the most plausible ORF and the function of the protein encoded. In this study, we applied the TACT system to 19 574 non-redundant human transcripts registered in H-InvDB and evaluated its predictive power by the degree of agreement with human-curated functional annotation in H-InvDB. As a result, the TACT system could assign functional description to 12 559 transcripts (64.2%), the remainder being hypothetical proteins. Furthermore, the overall agreement of functional annotation with H-InvDB, including those transcripts annotated as hypothetical proteins, was 83.9% (16 432/19 574). These results show that the TACT system is useful for functional annotation and that the prediction of ORFs and protein functions is highly accurate and close to the results of human curation. TACT is freely available at http://www.jbirc.aist.go.jp/tact/.

Amino Acid Motifs↗
PubMed1996

The human homolog T of the mouse T(Brachyury) gene; gene structure, cDNA sequence, and assignment to chromosome 6q27.

We have cloned the human gene encoding the transcription factor T. T protein is vital for the formation of posterior mesoderm and axial development in all vertebrates. Brachyury mutant mice, which lack T protein, die in utero with abnormal notochord, posterior somites, and allantois. We have identified human T genomic clones and derived the mRNA sequence and gene structure. There is 91% amino acid identity between human and mouse T proteins overall and complete identity across 77 amino acids of the T-box motif within the DNA-binding domain. Human T expression is very similar to that found for T in other vertebrate species and is confined to cells derived from the notochord. The human T gene maps to chromosome 6q27 and is only the second human member of the T-box gene family to be described.

Amino Acid Sequence↗