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PubMed1988

Chemical cross-linking of Sm and RNP antigenic proteins.

Nuclear extracts, competent for in vitro premessenger RNA splicing, were chemically cross-linked with thiol-reversible reagents in order to study the organization of proteins within ribonucleoprotein particles (RNPs) containing uridine-rich small nuclear RNAs (UsnRNPs). The distribution of select UsnRNP antigens within cross-linked complexes was determined by Western blotting of diagonal two-dimensional gels. On the basis of calculations from the molecular weights of cross-linked complexes containing UsnRNP common proteins B', B, and D, it is proposed that each of these proteins was associated with UsnRNP common proteins E and G. In addition, D' is proposed to be positioned close to D. The spatial distribution of UsnRNP common proteins was such that B' and B could not be cross-linked to D. The data also suggested that the 63-kDa U1 snRNP specific protein was cross-linked to other U1-specific proteins, particularly C, but not to the UsnRNP common proteins. We propose that part of the UsnRNP core of common proteins contains at least two asymmetrical copies of B':B:D:D':E:G with stoichiometries of 2:1:1:1:1:1 and 1:2:1:1:1:1.

Cell Nucleus↗
PubMed1988

Human placental fibronectin: demonstration of structural differences between the A and B chains in the extra domain-A region.

Fibronectins are a class of cell adhesion proteins produced from a single gene. Soluble plasma fibronectin plays a role in wound healing and the insoluble cellular fibronectin form anchors cells to the substrata. The proteins possess multiple macromolecular binding domains including collagen, fibrin, and heparin. Alternative RNA splicing in at least three regions (ED-A, ED-B, and III CS) is responsible for this fibronectin polymorphism. We have been studying this polymorphism at the protein level in placental fibronectin, a poorly soluble form of cellular fibronectin. Cathepsin D-digested placental fibronectin applied to a heparin-agarose column and eluted with a NaCl stepwise gradient (0.1, 0.3, 0.5 M) gave two polypeptides (80-100 and 65 kDa) in the 0.3 M NaCl peak. Immunoblots with monoclonal antibodies IST-2 (specific for the carboxy-terminal heparin-binding domain) and IST-9 (specific for the ED-A portion of fibronectin) suggest that both peptides contain the carboxy-terminal heparin-binding (Hep-2) domain, but that only the larger fragment possesses the ED-A segment. The two peptides were separated using sodium dodecyl sulfate-polyacrylamide gel electrophoresis, electrotransferred to Polybrene-coated polyvinyl difluoride membranes, and characterized by microsequence analysis. This analysis confirmed that both fragments start with the same amino acid sequence, 17 amino acids before the start of ED-A. These results demonstrate that placental fibronectin is a heterodimer, structurally distinct from plasma fibronectin due to the presence of a unique domain modification that is not seen in the plasma form.

Base Sequence↗
PubMed1993

Two isoforms of the EP3 receptor with different carboxyl-terminal domains. Identical ligand binding properties and different coupling properties with Gi proteins.

Functional cDNA clones for two isoforms of the mouse prostaglandin E receptor EP3 subtype derived from alternative RNA splicing were obtained. The two isoforms are only different in the sequence of the putative cytoplasmic carboxyl-terminal tail and their hydrophobicity; one isoform, named EP3 alpha, has a hydrophilic tail, and the other, named EP3 beta, has a hydrophobic tail. When expressed, the two receptors displayed identical ligand binding properties but different responses to guanosine 5'-O-(3-thiotriphosphate) (GTP gamma S). Without a change in the Bmax value, GTP gamma S increased Kd for prostaglandin E2 of EP3 beta and decreased that of EP3 alpha. These effects were abolished by the treatment of membranes with pertussis toxin and restored by the addition of Gi2. Although both isoforms exerted inhibition of forskolin-induced cAMP accumulation, three orders lower concentrations of agonists were required for EP3 alpha than EP3 beta for 50% inhibition of cAMP formation. A similar difference in agonist potency was observed also for agonist-induced stimulation of GTPase activity in membranes. Thus, the two receptors with different carboxyl-terminal tails show different coupling to the Gi protein, leading to the opposite responses to GTP in the ligand binding affinity and to different affinities of the agonist-occupied receptors to the G proteins.

Adenylyl Cyclases↗
PubMed1992

Organization, structure, and function of 95 kb of DNA spanning the murine T-cell receptor C alpha/C delta region.

We have analyzed the organization, structure, and function of the murine T-cell receptor C alpha/C delta region. This region spans 94.6 kb of DNA and contains the C alpha and C delta genes, as well as the V delta 5, J delta 2, and 50 different J alpha gene segments. Within this sequence we have identified 15 new J alpha gene segments, 40 new 5' RNA splice signals, and 40 new DNA rearrangement signals for the J alpha gene segments. The murine C alpha/C delta sequence contains an exceptionally high level of coding sequence with over 5.7% of the total sequence found in the exons. This is much more than that found in the beta-globin locus and the HPRT locus. Using the sequence data obtained from the C alpha/C delta region, we have designed simple assays to test for J alpha gene segment transcription and to determine the level of polymorphism for simple repeat sequences among different inbred strains of mice using the polymerase chain reaction. Furthermore, comparisons of this 95 kb of sequence with the available sequence from homologous regions of other species have led to the identification of a highly conserved sequence that is present throughout vertebrates and in the mouse binds lymphocyte-specific nuclear proteins. Comparisons of a 10-kb region, which includes the C alpha gene in human and mouse, average 66% sequence similarity. These studies support the contention that large-scale DNA sequencing projects of homologous regions of mouse and human will provide powerful new tools for studying the biology and evolution of loci such as the T-cell receptor and for identifying and posing new questions about the functions of conserved sequences.

Amino Acid Sequence↗
PubMed1992

Phosphorylation of cyclic adenosine 3',5'-monophosphate (cAMP) response element-binding protein isoforms by the cAMP-dependent protein kinase.

The cAMP response element-binding protein (CREB) mediates transcriptional activation of genes in response to the cAMP signal transduction pathway. There are two different isoforms of CREB, which are generated by alternative RNA splicing. There is evidence that the two isoforms may have different biological activities. As the longer isoform (CREB341) contains a potential phosphorylation site that is not present in the shorter isoform (CREB327), we examined the possible differential phosphorylation of the two CREB isoforms. Recombinant CREB was prepared and used as substrate for phosphorylation by the cAMP-dependent protein kinase in vitro. Phosphopeptide mapping and mutagenesis studies demonstrated that CREB341 contains two sites, serine 133 and serine 98, that can be phosphorylated in vitro by the catalytic subunit of the cAMP-dependent protein kinase. In contrast, CREB327 contains only a single phosphorylation site at serine 119 (equivalent position to serine 133 in CREB341). A kinase titration experiment demonstrated that serine 98 of CREB341 was phosphorylated only at relatively high concentrations of the cAMP-dependent protein kinase. Transient transfection studies were used to test for any possible function of the phosphorylation of serine 98 of CREB341. These studies used GAL4-CREB fusion proteins. We found that mutation of serine 98 to alanine (which would block phosphorylation) has little or no effect on the ability of the CREB fusion protein to activate transcription. These findings suggest that differences in the biological activity of the two CREB isoforms are probably not mediated by differential phosphorylation by the cAMP-dependent protein kinase.

Amino Acid Sequence↗
PubMed1999

Acidic and basic troponin T isoforms in mature fast-twitch skeletal muscle and effect on contractility.

Developmentally regulated alternative RNA splicing generates distinct classes of acidic and basic troponin T (TnT) isoforms. In fast-twitch skeletal muscles, an acidic-to-basic TnT isoform switch ensures basic isoform expression in the adult. As an exception, an acidic segment in the NH2-terminal variable region of adult chicken breast muscle TnT isoforms is responsible for the unique exclusive expression of acidic TnTs in this muscle (O. Ogut and J.-P. Jin. J. Biol. Chem. 273: 27858-27866, 1998). To understand the relationship between acidic vs. basic TnT isoform expression and muscle contraction, the contractile properties of fibers from adult chicken breast muscle were compared with those of the levator coccygeus muscle, which expresses solely basic TnT isoforms. With use of Triton X-100-skinned muscle fibers, the force and stiffness responses to Ca2+ were measured. Relative to the levator coccygeus muscle, the breast muscle fibers showed significantly increased sensitivity to Ca2+ of force and stiffness with a shift of approximately 0.15 in the pCa at which force or stiffness was 50% of maximal. The expression of tropomyosin, troponin I, and troponin C isoforms was also determined to delineate their contribution to thin-filament regulation. The data indicate that TnT isoforms differing in their NH2-terminal charge are able to alter the sensitivity of the myofibrillar contractile apparatus to Ca2+. These results provide evidence linking the regulated expression of distinct acidic and basic TnT isoform classes to the contractility of striated muscle.

Aging↗
PubMed1991

Human plasma fibronectin. Demonstration of structural differences between the A- and B-chains in the III CS region.

Fibronectins are a class of cell-adhesion proteins produced from a single gene. The soluble plasma form is synthesized by hepatocytes and the insoluble cellular form by fibroblasts and other cell types. The proteins possess multiple binding domains for macromolecules including collagen, fibrin and heparin along with at least one cell-binding domain. Cellular as well as plasma fibronectins are dimers of similar but not identical polypeptides. Their differences are the result of internal amino acid sequence variability due to alternative RNA splicing in at least three regions (ED-A, ED-B and III CS). We have been studying this polymorphism at the protein level in plasma fibronectin (pFn). Cathepsin D-digested pFn applied to a heparin-agarose column and eluted with an NaCl stepwise gradient (0.1 M, 0.25 M and 0.5 M) released two polypeptides (75 kDa and 65 kDa) in the 0.5 M-NaCl peak. Immunoblots with monoclonal antibodies IST-2 (specific for the C-terminal heparin-binding domain) and AHB-3 (specific for the III CS domain) suggest that both peptides contain the C-terminal heparin-binding (Hep-2) domain, but that only the larger fragment possesses the III CS region. These two polypeptides (75 kDa and 65 kDa) were digested with trypsin, and the resulting peptides were analyzed by fast-atom-bombardment mass spectrometry and compared with the known cDNA-derived peptide sequence. Peptides that were unique to the III CS region were further characterized by micro sequence analysis. The 75 kDa fragment is derived from the A-chain and contains the III CS region (89 amino acid residues) along with the C-terminal heparin-binding (Hep-2) domain and the fibrin-binding (Fib-2) domain. A single galactosamine-based carbohydrate group was detected at Thr-73/74 of the III CS region present in the 75 kDa fragment. The 65 kDa fragment is derived from the B-chain and lacks the entire III CS region but does contain the Hep-2 and Fib-2 domains.

Alkylation↗
PubMed1981

The organization and evolution of cloned globin genes.

The globin genes represent a complex set of sequences that are expressed in a coordinate fashion during the development of red blood cells. while this complex family of genes may consist of as many as ten to fourteen members [34], three of these genes have now been cloned and their entire nucleotide sequence determined. As was initially observed in the case of beta globin major gene, all are encoded in three distinct coding blocks separated by two intervening sequences of DNA. Their intervening sequences of DNA are preserved, with respect to location, but are widely divergent, with respect to size and sequence. The divided information in each gene is edited and spliced together at the level of its initial RNA transcript which is complementary to the entire gene sequence including its intervening sequences. Structural correlation analyses have allowed us to identify sites in all three genes that might be responsible for the initiation of transcription, RNA splicing, and poly A addition. The function of these sites has been tested by cloning these genes in an animal virus vector SV40. Such animal virus hybrids have been used to infect tissue culture cells and have directed the synthesis of both alpha and beta mouse globin in cells of monkey origin. These studies indicate that such signals operate across species barriers and further indicate that the animal virus vector system will be useful in elucidating their function.

Amino Acid Sequence↗
PubMed1983

Fate of an intervening sequence ribonucleic acid: excision and cyclization of the Tetrahymena ribosomal ribonucleic acid intervening sequence in vivo.

In previous studies of RNA splicing in vitro, we have shown that the intervening sequence (IVS) of the Tetrahymena rRNA precursor is excised as a unique linear RNA molecule and subsequently cyclized. In the present work, we have investigated the occurrence and stability of these RNA species in vivo. RNA was separated by gel electrophoresis, transferred to diazotized paper, and hybridized with 32P-labeled DNA probes. RNA molecules containing the IVS were found to reside within the nucleus and not in the cytoplasm. The species found in nucleus include both the linear and circular forms of the excised IVS RNA, as well as the unspliced precursor. On the basis of quantitation of the hybridization, the half-lives of the IVS-containing pre-rRNA and the excised IVS RNA in rapidly growing cells were estimated as 2 and 6 s, respectively. We conclude that splicing is not a rate-limiting step in rRNA maturation and that the IVS RNA is quickly degraded after its excision. When the deproteinized nuclear RNA was incubated at 37 degrees C in a Mg2+-containing solution, a substantial portion of the linear IVS RNA was converted to the circular form. Autocyclization, previously characterized with IVS RNA produced by splicing in vitro, is therefore also a property of IVS RNA produced in vivo.

Animals↗
PubMedDate not supplied

The equilibrium partition function and base pair binding probabilities for RNA secondary structure.

A novel application of dynamic programming to the folding problem for RNA enables one to calculate the full equilibrium partition function for secondary structure and the probabilities of various substructures. In particular, both the partition function and the probabilities of all base pairs are computed by a recursive scheme of polynomial order N3 in the sequence length N. The temperature dependence of the partition function gives information about melting behavior for the secondary structure. The pair binding probabilities, the computation of which depends on the partition function, are visually summarized in a "box matrix" display and this provides a useful tool for examining the full ensemble of probable alternative equilibrium structures. The calculation of this ensemble representation allows a proper application and assessment of the predictive power of the secondary structure method, and yields important information on alternatives and intermediates in addition to local information about base pair opening and slippage. The results are illustrated for representative tRNA, 5S RNA, and self-replicating and self-splicing RNA molecules, and allow a direct comparison with enzymatic structure probes. The effect of changes in the thermodynamic parameters on the equilibrium ensemble provides a further sensitivity check to the predictions.

Animals↗
PubMed2000

Genotype-specific synthesis and secretion of spliced hepatitis B virus genomes in hepatoma cells.

Hepatitis B virus-infected patients frequently have viral particles with DNA derived from differently spliced RNA. Which factors influence the synthesis of these splice variants is unclear. We analysed the type of splice variants produced from different genotypes and determined whether they are secreted as efficiently as wild-type virus. We demonstrate production of a single splice variant from genotypes D, C, and E as dominant species in two hepatoma cell lines. The type of minor splice variants synthesised varied between genotypes but was identical in both hepatoma cell lines. A novel splice variant with a deletion in the core gene was identified for genotype D. Viral DNA from intracellular compared with extracellular viral particles was spliced approximately five times more often than wild-type-sized genomes. A variable amount of the major splice variant was also identified in sera from patients infected with genotypes A, D, and C. These data indicate genotype A-, C-, D-, and E- as well as hepatoma cell line-independent synthesis of a dominant single splice variant and argue for a biological function of the corresponding splice sites. This study clearly demonstrates the intracellular accumulation of viral particles containing spliced genomes and offers a tool for the investigation of underlying mechanisms.

Alternative Splicing↗
PubMed1986

HTLV-III expression and production involve complex regulation at the levels of splicing and translation of viral RNA.

The African green monkey nonlymphoid cell line cos-1 produces infectious HTLV-III virus following transfection with biologically active molecular clones of HTLV-III. Transfected cos-1 cells produce large amounts of viral RNA and protein. We have used this rapid transfection system to study the regulatory functions and synthetic capacity of the HTLV-III genome, as well as mutants derived from it. Analysis of transfected lymphoid and nonlymphoid cell lines suggests that tat-III-mediated trans-activation of viral gene expression is operative predominantly, if not exclusively, at a posttranscriptional level. We have also identified an additional HTLV-III-encoded gene that controls viral gene expression through regulation of the relative proportions of the various viral RNA transcripts and is required for viral replication.

Animals↗
PubMed2006

Characterization of a spliced exon product of herpes simplex type-1 latency-associated transcript in productively infected cells.

The latency-associated transcripts (LATs) of herpes simplex virus type-1 (HSV-1) are the only viral RNAs accumulating during latent infections in the sensory ganglia of the peripheral nervous system. The major form of LAT that accumulates in latently infected neurons is a 2 kb intron, spliced from a much less abundant 8.3 primary transcript. The spliced exon mRNA has been hard to detect. However, in this study, we have examined the spliced exon RNA in productively infected cells using ribonuclease protection (RPA), and quantitative RT-PCR (q-PCR) assays. We were able to detect the LAT exon RNA in productively infected SY5Y cells (a human neuronal cell line). The level of the LAT exon RNA was found to be approximately 5% that of the 2 kb intron RNA and thus is likely to be relatively unstable. Quantitative RT-PCR (q-PCR) assays were used to examine the LAT exon RNA and its properties. They confirmed that the LAT exon mRNA is present at a very low level in productively infected cells, compared to the levels of other viral transcripts. Furthermore, experiments showed that the LAT exon mRNA is expressed as a true late gene, and appears to be polyadenylated. In SY5Y cells, in contrast to most late viral transcripts, the LAT exon RNA was found to be mainly nuclear localized during the late stage of a productive infection. Interestingly, more LAT exon RNA was found in the cytoplasm in differentiated compared to undifferentiated SY5Y cells, suggesting the nucleocytoplasmic distribution of the LAT exon RNA and its related function may be influenced by the differentiation state of cells.

Cell Differentiation↗
PubMed1996

An alternatively spliced C. elegans ced-4 RNA encodes a novel cell death inhibitor.

The C. elegans gene ced-4 is essential for programmed cell death. We report that ced-4 encodes two transcripts and that whereas the major transcript can cause programmed cell death, the minor transcript can act oppositely and prevent programmed cell death, thus defining a novel class of cell death inhibitors. That ced-4 has both cell-killing and cell-protective functions is consistent with previous genetic studies. Our results suggest that the dual protective and killer functions of the C. elegans bcl-2-like gene ced-9 are mediated by inhibition of the killer and protective ced-4 functions, respectively. We propose that a balance between opposing ced-4 functions influences the decision of a cell to live or to die by programmed cell death and that both ced-9 and ced-4 protective functions are required to prevent programmed cell death.

Alleles↗
PubMed1997

Comparison of the subcellular distribution of the messages encoding PLP and DM-20.

Oligonucleotides provide a means to differentiate between closely related mRNAs. Here in situ hybridization is performed using oligonucleotide probes to determine the subcellular distribution of two differential splicing products of a single gene. It is demonstrated here that the subcellular distributions of PLP and DM-20 messages in oligodendrocytes are quite different, despite being transcripts of a single gene.

Animals↗
PubMed1997

A new approach to investigating the relationship between productive infection and cytopathicity in vivo.

We describe a novel experimental approach to analyzing virus-host relationships and potential mechanisms of cytopathicity in vivo in simian immunodeficiency virus (SIV) infections. Progressive destruction of lymphoid tissue in the course of infection by SIV or human immunodeficiency virus (HIV) accompanies the loss of CD4+ T lymphocytes and sets the stage for AIDS. Because one of the important early events in this pathological process is lysis of follicular dendritic cells (FDCs), we investigated the controversial role of productive SIV infection in the destruction of FDCs. To differentiate productive infections from the known association of virus with FDCs as immune complexes trapped on cell surfaces, we used detection of spliced viral mRNAs in cells as evidence of productive infection. We found that spliced and unspliced viral RNAs could be detected by in situ hybridization (ISH) with specific antisense oligonucleotide probes in lymphocytes and macrophages with sensitivities of fewer than ten copies of spliced viral RNA per cell. We detected only unspliced RNA in germinal centers where FDCs reside. Thus, no productive infection of these cells can be detected in vivo by this assay, and their destruction likely occurs by indirect mechanisms that have yet to be determined.

Animals↗