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Transcription of adenovirus 5 early region 1b is elevated in permissive cells infected by a mutant with an upstream deletion.

Early region 1b (E1b) of adenovirus 5 consists of a single transcription unit that lies from 1,702 to 4,070 nucleotides from the conventional left end of the genome. The effect of mutations that map upstream of E1b on the production of E1b mRNA was examined in vivo with mutants defective in gene functions from the neighboring early region 1a (E1a) transcription unit (499 to 1,632 nucleotides from the left end). These host range mutants replicate in the adenovirus 5-transformed human cell line 293. E1b mRNA accumulation was assayed by DNA-RNA hybridization late after productive infection when the E1b transcripts are abundant in the cytoplasm. Cells infected by wild-type virus, mutant dl311, or mutant hr1. The elevated levels of E1b mRNA were also detected in steady-state nuclear RNA, pulse-labeled polyadenylated nuclear RNA, and pulse-labeled total nuclear RNA. These data indicate that E1b transcription was elevated in human 293 cells infected with dl312. There was no evidence of increases in genomic DNA in dl312-infected cells, suggesting that the rate of transcription may be elevated. When mixed infections with a 10-fold excess of either dl312 or wild-type virus were performed, the phenotype was that of the more abundant genome. This result suggests that the respective phenotypes were cis dominant. The increased rate of transcription can be attributed to cis-active regulatory effects of the deletion of nucleotides 448 to 1,349 in mutant dl312 DNA.

Adenoviruses, Human↗

Developmental aspects of uridine addition within mitochondrial transcripts of Trypanosoma brucei.

The mitochondrial respiratory system is absent in slender bloodstream forms of Trypanosoma brucei, incomplete in stumpy bloodstream forms, and complete in procyclic (insect) forms. The steady-state abundance of transcripts of some mitochondrially encoded components of the respiratory system correlates with its differential expression in different life cycle stages. Recently, it was reported that uridines which are not encoded in the genome are added to cytochrome b and cytochrome oxidase II transcripts. We now report that the (U)+ transcripts of both genes are found in procyclic forms and to some degree in stumpy forms but are absent in slender forms. The uridine additions to cytochrome oxidase II correct a frameshift in the gene and presumably allow production of a full-length protein, whereas those added to cytochrome b create an in-frame AUG which extends the N terminus of the predicted protein by 20 amino acids. The stage specificity of uridine additions to these transcripts thus reflects the life cycle stage during which the protein products would be used. Transcripts of MURF2, a gene of unknown function, have additional uridines in both slender and procyclic forms which create two in-frame AUGs. MURF2 transcripts additionally differ from the DNA sequence in ways which cannot be explained by uridine addition alone, implying that other processes alter these transcripts.

Animals↗

Expression of receptor protein tyrosine phosphatase-sigma (RPTP-sigma) in the nervous system of the developing and adult rat.

The expression of receptor protein tyrosine phosphatase-sigma (RPTP-sigma) mRNA during rat development was examined by Northern blot and in situ hybridization analyses. Northern blot analysis revealed that the two transcripts (5.7 kb and 6.9 kb) had different spatial and temporal patterns of expression. The 6.9-kb transcript was more abundant during embryonic development, whereas the 5.7-kb transcript was more abundant during postnatal development and in the adult. In situ hybridization revealed that RPTP-sigma mRNA was widely expressed throughout the central and peripheral nervous system during embryonic development. Very high levels were seen in the ventricular zone, subventricular zone, cortex, dorsal root ganglia, cranial nerve ganglia, olfactory epithelium, and retina. During postnatal development the level of expression decreased in most brain regions. However, high levels continued to be seen in the hippocampus. Emulsion autoradiography revealed that the majority of RPTP-sigma mRNA is expressed in neurons. Northern analysis showed that cultured glial cells expressed the 6.9-kb transcript, but not the 5.7-kb. RPTP-sigma mRNA expression profiles were clearly distinct from those of leukocyte antigen-related protein (LAR), a closely related RPTP. The spatiotemporal pattern of RPTP-sigma mRNA expression indicates that RPTP-sigma may play a role in the development of the nervous system.

Age Factors↗

Expression of the gut-enriched Krüppel-like factor gene during development and intestinal tumorigenesis.

We examined the expression of GKLF (gut-enriched Krüppel-like factor), a recently identified zinc finger-containing transcription factor, in mice during development using the ribonuclease protection assay. In the adult, the level of GKLF transcript is abundant throughout the gastrointestinal tract. Between embryonic days 10 and 19 (E10 and E19) of development, the initial level of whole embryo GKLF transcript is low but begins to rise on E13 and peaks on E17. In the newborn, GKLF transcript level is higher in the colon than in the small intestine although the levels in both organs rise with increasing age. Expression of GKLF was also examined in the intestinal tract of the Min mouse, a model of intestinal tumorigenesis. The level of GKLF transcript is significantly decreased in the intestine of Min mice during a period of tumor formation when compared to age-matched control littermates. Our findings indicate that GKLF expression correlates with certain periods of gut development and is down-regulated during intestinal tumorigenesis, suggesting that GKLF may play a role in gut development and/or tumor formation.

Animals↗

Developmental expression patterns of Beta-ig (betaIG-H3) and its function as a cell adhesion protein.

Beta-ig is a secretory protein embodied by fasciclin I-like repeats containing sequences that might bind integrins and glycosaminoglycans in vivo. Expression of Beta-ig is responsive to Transforming Growth Factor-beta and the protein is found to be associated with extracellular matrix (ECM) molecules, implicating Beta-ig as an ECM adhesive protein of developmental processes. The spatiotemporal distribution of Beta-ig during various stages of murine development was examined and its ability to support adhesion of various cell types assessed. In situ hybridization of mouse embryos (E12.5-E18.5) indicated a prominent, distinct expression pattern for Beta-ig message in connective tissue. Beta-ig transcripts were abundantly expressed during mesenchymal cell condensation in areas of axial, craniofacial and appendicular primordial cartilage from E12.5-E14.5. Beginning at E15.5, Beta-ig transcripts appeared in collagen-rich tissues, including dura mater and corneal stroma. During E16.5-E18.5, Beta-ig transcripts were observed in proliferating chondrocytes and areas of endochondral ossification in joint and articular cartilage formation. Connective tissues expressed Beta-ig transcripts within the nasal septum and surrounding cartilage primordia, and in the pericardium, optic cup, kidney, ovary, esophagus, diaphragm, bronchi, trachea and corneal epithelium, and during cardiac valve formation. These patterns of expression indicate that Beta-ig may be involved in tissue morphogenesis. Cells derived from mesenchyme attached onto a substratum comprised of purified recombinant Beta-ig. Taken together, the results indicate that Beta-ig is expressed principally in collagen-rich tissues where it may interact with cells and ECM molecules, perhaps playing a role in tissue morphogenesis.

Amino Acid Sequence↗

Joining chain-expressing and -nonexpressing B cell populations in the mouse.

The diphtheria toxin A chain (DTA) was gene targeted into the Joining chain (J chain) locus to create a mouse strain selecting against J chain-expressing cells, JDTA mice. Serum immunoglobulin (Ig)M and serum IgG were reduced six to eightfold, while serum IgA was elevated 14-fold in these mice. JDTA mice were immune competent although the serum Ig response compared with wild-type mice was reduced sixfold at day 14 but only fourfold at day 45 after immunization. Exchanging the DTA gene with a cDNA for c-myc resulted in mice with a distinct phenotype with increased Ig production and enhanced humoral immune responses. Analysis of single B cells stimulated by lipopolysaccharide in vitro using reverse transcription-polymerase chain reaction showed that J chain-nonexpressing B cells could be detected that had a secretory phenotype as determined by an abundance of transcript for secretory IgM. Finally, limiting dilution analysis of peripheral B cells showed that J chain expression was a clonal property already established in naive, peripheral B lymphocytes.

Animals↗

The activated Mlvi-4 locus in Moloney murine leukemia virus-induced rat T-cell lymphomas encodes an env/Mlvi-4 fusion protein.

A genomic DNA probe derived from the region immediately 3' of the clusters of integrated proviruses in the Mlvi-4 locus detects a 5.5-kb mRNA transcript which is specifically expressed in normal rat thymus and spleen. The same probe detects two tumor-specific mRNA transcripts 2.5 and 10 kb long, both of which are expressed only in tumors carrying a provirus in the Mlvi-4 locus. Sequence analysis of two cDNA clones (LE3a and B1.1) of the 2.5-kb tumor-specific mRNA, obtained from two independent tumors (6889 and B1), revealed that they are both derived from hybrid env/Mlvi-4 mRNA transcripts. The splicing of env to Mlvi-4 sequences linked a cryptic splice donor site at nucleotide position 6397 of the viral genome with a splice acceptor site in the region immediately 3' of the integrated provirus. The mRNA that gives rise to cDNA clone B1.1 terminates 1,005 bases 3' of the splice acceptor site without additional splicing. The mRNA that gives rise to cDNA clone LE3a terminates in the same site but undergoes differential splicing of an 81-base-long intron. The resulting mRNAs contain 247-amino-acid (clone B1.1) or 226-amino-acid (clone LE3a) open reading frames sharing 221 N-terminal amino acids, of which 207 are derived from the viral env gene and 14 are derived from Mlvi-4. RNase protection assays using 6889 tumor cell RNA and a probe derived from the cDNA clone LE3a detected both mRNA transcripts. More abundant of the two, however, was the one encoding the putative 247-amino-acid protein. Transient transfections of a construct expressing the RNA transcript defined by clone B1.1 into D17 cells led to the expression of an Env/Mlvi-4 fusion protein with an apparent molecular mass of 33 kDa. Given that cells with provirus insertions in the Mlvi-4 locus are selected and that retroviral env gene products may have profound effects in the biology of hematopoietic cells, we suggest that the detected fusion proteins may contribute to the growth of T-cell lymphomas.

Amino Acid Sequence↗

A heat-labile factor promotes premature 3' end formation in exon 1 of the murine adenosine deaminase gene in a cell-free transcription system.

An elongation block to RNA polymerase II transcription in exon 1 is a major regulatory step in expression of the murine adenosine deaminase (ADA) gene. Previous work in the laboratory identified abundant short transcripts with 3' termini in exon 1 in steady-state RNA from injected oocytes. Using a cell-free system to investigate the mechanism of premature 3' end formation, we found that polymerase II generates prominent ADA transcripts approximately 96 to 100 nucleotides in length which are similar to the major short transcripts found in steady-state RNA from oocytes injected with ADA templates. We have determined that these transcripts are the processed products of 108- to 112-nucleotide precursors. Precursor formation is (i) favored in reactions using circular templates, (ii) not the result of a posttranscriptional processing event, (iii) sensitive to low concentrations of Sarkosyl, and (iv) dependent on a factor(s) which is inactivated in crude extracts at 47 degrees C for 15 min. The cell-free system will allow further characterization of the template and factor requirements involved in the control of premature 3' end formation by RNA polymerase II.

Adenosine Deaminase↗

von Hippel-Lindau protein-mediated repression of tumor necrosis factor alpha translation revealed through use of cDNA arrays.

Based on evidence that the von Hippel-Lindau (VHL) tumor suppressor protein is associated with polysomes and interacts with translation regulatory factors, we set out to investigate the potential influence of pVHL on protein translation. To this end, renal cell carcinoma (RCC) cells that either lacked pVHL or expressed pVHL through stable transfection were used to prepare RNA from cytosolic (unbound) and polysome-bound fractions. Hybridization of cDNA arrays using RNA from each fraction revealed a subset of transcripts whose abundance in polysomes decreased when pVHL function was restored. The tumor necrosis factor alpha (TNF-alpha) mRNA was identified as one of the transcripts that preferentially associated with polysomes in pVHL-deficient cells. Additional evidence that the TNF-alpha mRNA was a target of translational repression by pVHL was obtained from reporter gene assays, which further revealed that pVHL's inhibitory influence on protein synthesis occurred through the TNF-alpha 3'-untranslated region. Our findings uncover a novel function for the pVHL tumor suppressor protein as regulator of protein translation.

3' Untranslated Regions↗

Histidine tRNA from chicken mitochondria has an uncoded 5'-terminal guanylate residue.

In an attempt to identify the transcription initiation sites in chicken mitochondrial DNA, RNAs capped in vitro using vaccinia guanylyl transferase and [alpha-32P] GTP were analyzed. The most abundant labeled transcript was identified by RNA sequencing as the mitochondrial tRNA(His). Sequence analysis also revealed that this tRNA contains an extra guanylate residue at its 5' end, characteristic of the histidine tRNA family. The respective genomic region was also cloned and sequenced. In contrast to bacteria and the mitochondria of fungi and plants, the extra G of chicken mitochondrial tRNA(His) is not encoded in the gene. Therefore, the guanylate residue must be added post-transcriptionally, as demonstrated for the nuclear tRNA(His) in yeast and Drosophila. Analysis of a capped tRNA(His) precursor of chicken mitochondria suggests that addition of the extra G occurs independently of 3' end maturation. Since in the chicken mitochondrial tRNA(His) the extra G can be efficiently labeled by the capping assay, it should possess a 5'-terminal di- or triphosphate, which contrasts to the 5'-terminal monophosphate proposed for the nuclear encoded tRNA(His). Our results imply that the ability of a mitochondrial RNA to be capped in vitro does not necessarily prove that it contains a transcription initiation site.

Animals↗

Genetic organization and mRNA expression of enolase genes of Candida albicans.

In previous work, we cloned a Candida albicans cDNA for the glycolytic enzyme enolase and found a single, abundant enolase transcript on Northern (RNA) blots and a single protein on immunoblots, using antiserum raised against a recombinant enolase fusion protein. Because C. albicans enolase is abundantly produced during infection and elicits strong host immune responses, the mechanisms regulating enolase production are important for understanding the growth of C. albicans in vivo. To obtain more information on enolase gene expression by C. albicans, we used the enolase cDNA clone to investigate the genetic organization of enolase genes and the steady-state levels of enolase mRNA under several growth conditions. Gene disruption techniques in combination with Southern blot analyses of genomic DNA showed the presence of two enolase gene loci that could be distinguished by the locations of ClaI and Mn/I sites in their 3' flanking regions. Enolase steady-state mRNA levels were greatest during the middle phase of the logarithmic growth curve and were low during stationary phase. Minimal differences in enolase mRNA levels between yeast cells and hyphae were found. Propagation of C. albicans in glucose did not cause increased enolase mRNA levels compared with growth in a nonfermentable carbon source (pyruvate). It was concluded that two gene loci exist for C. albicans enolase and that enolase mRNA is constitutively produced at high levels during active metabolism.

Blotting, Southern↗

Microarray analysis of genes showing variable expression following a blood meal in Anopheles gambiae.

A microarray analysis of 14 900 genes of the malaria vector mosquito, Anopheles gambiae, shows that as many as 33% (4924) of their corresponding transcription products vary in abundance within 24 h after a blood meal. Approximately half (2388) of these products increase in their accumulation and the remainder (2536) decrease. Expression dynamics of 80% of the genes analysed by expressed sequence tag (EST) projects reported previously are consistent with the observations from this microarray analysis. Furthermore, the microarray analysis is more sensitive in detecting variation in abundance of gene products expressed at low levels and is more sensitive overall in that a greater number of regulated genes are detected. Major changes in transcript abundance were seen in genes encoding proteins involved in digestion, oogenesis and locomotion. The microarray data and an electronic hyperlinked version of all tables are available to the research community at http://www.angagepuci.bio.uci.edu/1/.

Animals↗

Ordered assembly of mitochondria during rice germination begins with pro-mitochondrial structures rich in components of the protein import apparatus.

Mitochondrial maturation during imbibition of rice embryos follows the transition of unstructured double membrane bound pro-mitochondria to the typical cristae-rich mitochondrial structures observed in mature plant cells. During the first 48 h following imbibition, an ordered increase in the abundance of transcripts encoding mitochondrial proteins was observed. Co-incident with these changes in transcript levels was dynamic and rapid changes in mitochondrial protein content and mitochondrial function. Proteins representing components of the mitochondrial protein import apparatus are strikingly abundant in dry seeds, and a functional import apparatus was shown to operate 2 h after imbibition. Interestingly, this import process was best driven by the oxidation of NADH from outside the mitochondrial inner membrane. In later developmental stages the capacity for matrix organic acid metabolism was evident, accompanied by the appearance of proteins for TCA cycle components, and coordination of electron transport chain assembly through components encoded in both mitochondrial and nuclear genomes. Together these events provide new insights into the understanding of mitochondrial maturation and the nature of pro-mitochondrial structures in plant cells.

Blotting, Western↗

A conserved His-Asp signal response regulator-like gene in Heterosigma akashiwo chloroplasts.

Regulation of gene expression in plastids may involve molecular components conserved from cyanobacteria-like ancestors. Among prokaryotes, genes are commonly regulated at the transcriptional level by 'two-component' or 'His-Asp' signal transducers, consisting of a 'sensor kinase', which autophosphorylates at a conserved histidine residue, and a cognate response regulator, which is phosphorylated by the sensor kinase at a conserved aspartate residue. A putative His-Asp response regulator gene (trg1: transcriptional regulatory gene 1) has been identified in the estuarine raphidophytic alga Heterosigma akashiwo. The chloroplast-encoded trg1 is 693 bp in length, contains no introns, and yields a conceptual translation product of 231 amino acids, with a predicted mass of 27 kDa. Homology searches suggest that Heterosigma trgl has an omnpR-like identity within the DNA-binding His-Asp family of response regulators. trg1 contains both the phosphorylation and DNA-binding domains which are present in prokaryote response regulators. Quantitative competitive RT-PCR showed that Heterosigma trg1 is expressed at low levels (5 microg per g total RNA). In contrast, psbA (a photosystem II component) transcript is abundant (60 mg per g total RNA). Cell cycle analysis showed that psbA abundance oscillates in response to light but trg1 mRNA levels are invariant. We hypothesize that a His-Asp phosphorelay mechanism may affect chloroplast genome transcription in a manner similar to bacterial signal transduction pathways in which 'sensor kinase' and cognate 'response regulator' proteins interact.

Algal Proteins↗

The major protein import receptor of plastids is essential for chloroplast biogenesis.

Light triggers the developmental programme in plants that leads to the production of photosynthetically active chloroplasts from non-photosynthetic proplastids. During this chloroplast biogenesis, the photosynthetic apparatus is rapidly assembled, mostly from nuclear-encoded imported proteins, which are synthesized in the cytosol as precursors with cleavable amino-terminal targeting sequences called transit sequences. Protein translocon complexes at the outer (Toc complex) and inner (Tic complex) envelope membranes recognize these transit sequences, leading to the precursors being imported. The Toc complex in the pea consists of three major components, Toc75, Toc34 and Toc159 (formerly termed Toc86). Toc159, which is an integral membrane GTPase, functions as a transit-sequence receptor. Here we show that Arabidopsis thaliana Toc159 (atToc159) is essential for the biogenesis of chloroplasts. In an Arabidopsis mutant (ppi2) that lacks atToc159, photosynthetic proteins that are normally abundant are transcriptionally repressed, and are found in much smaller amounts in the plastids, although ppi2 does not affect either the expression or the import of less abundant non-photosynthetic plastid proteins. These findings indicate that atToc159 is required for the quantitative import of photosynthetic proteins. Two proteins that are related to atToc159 (atToc120 and atToc132) probably help to maintain basal protein import in ppi2, and so constitute components of alternative, atToc159-independent import pathways.

Amino Acid Sequence↗

Transcriptional responses in the hemiparasitic plant Triphysaria versicolor to host plant signals.

Parasitic plants in the Scrophulariaceae use chemicals released by host plant roots to signal developmental processes critical for heterotrophy. Haustoria, parasitic plant structures that attach to and invade host roots, develop on roots of the hemiparasitic plant Triphysaria versicolor within a few hours of exposure to either maize (Zea mays) root exudate or purified haustoria-inducing factors. We prepared a normalized, subtractive cDNA library enriched for transcripts differentially abundant in T. versicolor root tips treated with the allelopathic quinone 2,6-dimethoxybenzoquinone (DMBQ). Northern analyses estimated that about 10% of the cDNAs represent transcripts strongly up-regulated in roots exposed to DMBQ. Northern and reverse northern analyses demonstrated that most DMBQ-responsive messages were similarly up-regulated in T. versicolor roots exposed to maize root exudates. From the cDNA sequences we assembled a unigene set of 137 distinct transcripts and assigned functions by homology comparisons. Many of the proteins encoded by the transcripts are predicted to function in quinone detoxification, whereas others are more likely associated with haustorium development. The identification of genes transcriptionally regulated by haustorium-inducing factors provides a framework for dissecting genetic pathways recruited by parasitic plants during the transition to heterotrophic growth.

Benzoquinones↗

A Pituitary cell type coexpressing messenger ribonucleic acid of proopiomelanocortin and the glycoprotein hormone alpha-subunit in neonatal rat and chicken: rapid decline with age and reappearance in vitro under regulatory pressure of corticotropin-releasing hormone in the rat.

Promiscuous hormone mRNA expression in the pituitary remains poorly understood. We examined by means of RT-PCR and immunostaining whether glycoprotein hormone alpha-subunit (alphaGSU) could be coexpressed with proopiomelanocortin (POMC) in vivo and under pressure of CRH in vitro. Cells coexpressing alphaGSU and POMC mRNA amounted to 2.6% of the cells in ex vivo rat pituitary at birth [postnatal d 1 (P1)], fell to much lower level at P14, and were undetectable in adulthood. In cultured pituitary aggregates of P14 rats, alphaGSU/POMC cells remained scarce but represented up to 6.6% after chronic treatment with CRH but not leukemia inhibitory factor. CRH was less effective in aggregates from P1 and adult rats. The total alphaGSU population ex vivo at P1 was two times smaller than at P14, but in culture it expanded 2.5 times, concomitantly with a reciprocal change in POMC cell abundance. Tpit transcripts were detected in POMC-only and alphaGSU/POMC cells but not in alphaGSU-only cells. Cells coexpressing alphaGSU and POMC mRNA were relatively abundant in P14 chicken pituitary and aggregate cultures, but occurrence was not affected by CRH. Immunostaining showed alphaGSU and POMC colocalization in sporadic cells in intact rat pituitary and CRH-treated cultures at P1 but not at P14 and adult age. The data demonstrate the occurrence of cells coexpressing alphaGSU and POMC in rat and chicken pituitary. The developmental dynamics of this cell population and its response to CRH in vitro in the rat suggest a relationship of these cells with the embryonic branching of the POMC and alphaGSU cell lineages and their mutually opposite developmental course during early postnatal life.

Aging↗

Quantitative in situ localization of tenascin-C alternatively spliced transcripts in the avian optic tectum.

PURPOSE: Tenascin-C is an extracellular matrix glycoprotein found at sites of embryonic cell motility, including the developing visual system. Numerous alternatively spliced variants of tenascin-C have been identified, and these variants have distinctive properties in vitro. The purpose of this study was to use quantitative in situ hybridization to determine the relative abundance of transcripts encoding the alternatively spliced fibronectin type III repeats of tenascin-C in the embryonic avian optic tectum. METHODS: Similarly sized DNA probes specific for sequences encoding the alternatively spliced repeats of tenascin-C were labeled with 35-S and applied to frozen sections of the E10 optic tectum. After determining the linear period of exposure, silver grain densities in the ventricular zone were calculated. RESULTS: Densitometric analysis revealed that more than half of the total tenascin-C mRNAs expressed in the ventricular zone of the E10 optic tectum encode the variable fibronectin type III repeats "A," "AD1" and "D." Transcripts encoding other variable repeats were detectable, but at considerably lower levels. CONCLUSIONS: The most abundant form of tenascin-C in the developing optic tectum has a molecular weight of 230 kDa. Most of this form contains the variable repeats "A," "AD1," and "D," a combination of fibronectin type III repeats that has previously been identified only in a tumor-derived cell line.

Alternative Splicing↗