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PubMed1990

Coupling of DNA replication to growth rate in Escherichia coli: a possible role for guanosine tetraphosphate.

Two promoters for the Escherichia coli operon that contains the four genes dnaA, dnaN, recF, and gyrB were found to be growth rate regulated and under stringent control. Transcript abundance relative to total RNA increased with the growth rate. Changes in transcription from the dnaAp1 and dnaAp2 promoters that were induced by amino acid starvation and chloramphenicol and were relA dependent were correlated with the stringent response. The abundance of these transcripts per total RNA also decreased in spoT mutants as the severity of the mutation increased (guanosine 5'-diphosphate 3'-diphosphate [ppGpp] basal levels increased). Because expression of these promoters appears to be inhibited by ppGpp, it is proposed that one mechanism for coupling DNA replication to the growth rate of bacteria is through ppGpp synthesis at the ribosome.

DNA Replication↗
PubMed1996

Equalizing cDNA subtraction based on selective suppression of polymerase chain reaction: cloning of Jurkat cell transcripts induced by phytohemaglutinin and phorbol 12-myristate 13-acetate.

The major drawback of subtractive cDNA libraries is that the original disproportion in concentrations of different types of transcripts is preserved. This usually makes the isolation of specific rare transcripts extremely difficult. To overcome this difficulty, we propose a strategy that introduces the equalization of concentrations (normalization) of specific transcripts during the subtractive process. This makes possible obtaining both rare and highly abundant transcripts in the resulting subtracted library. This technique has been applied for isolation of transcripts activated upon induction of Jurkat cells by phytohemaglutinin and phorbol 12-myristate 13-acetate. Six novel up-regulated sequences belonging to a low-abundance class of transcripts have been obtained.

Blotting, Northern↗
PubMed1994

Identification and characterization of the developmentally regulated pattern of expression in the testis of a mouse gene exhibiting similarity to the family of phosphodiesterases.

A cDNA for a rat brain phosphodiesterase (PDE) was used to screen a mouse testis library to identify the murine PDEs which are expressed in this tissue. A clone of 981 bp, p4-6, was isolated and shown to exhibit limited identity at the amino acid level to the rat brain PDE (20%). The putative protein encoded by clone p4-6 also contains multiple potential modification sites, for phosphorylation, myristylation, and glycosylation, many of which are located at positions similar to those found for rat brain PDE. The gene identified by p4-6 yields 3 transcripts, an abundant 1.9 kb transcript, and less abundant transcripts of 3.8 and 6.7 kb. Of the nine tissues examined in this study, the expression of the corresponding gene was limited to the adult mouse testis. Furthermore, the expression in the testis was most abundant in the germ cell lineage, although low levels were detected in somatic cells of the testis as well. Analysis of RNA from testes at different stages of development suggested that the p4-6 gene is most abundantly expressed in germ cells that have completed the meiotic divisions.

Amino Acid Sequence↗
PubMed1999

Diurnal variations in hydraulic conductivity and root pressure can be correlated with the expression of putative aquaporins in the roots of lotus japonicus

The hydraulic conductivity of excised roots (Lp(r)) of the legume Lotus japonicus (Regel) K. Larsen grown in mist (aeroponic) and sand cultures, was found to vary over a 5-fold range during a day/night cycle. This behaviour was seen when Lp(r) was measured in roots exuding, either under root pressure (osmotic driving force), or under an applied hydrostatic pressure of 0.4 MPa which produced a rate of water flow similar to that in a transpiring plant. A similar daily pattern of variation was seen in plants grown in natural daylight or in controlled-environment rooms, in plants transpiring at ambient rates or at greatly reduced rates, and in plants grown in either aeroponic or sand culture. When detached root systems were connected to a root pressure probe, a marked diurnal variation was seen in the root pressure generated. After excision, this circadian rhythm continued for some days. The hydraulic conductivity of the plasma membrane of individual root cells was measured during the diurnal cycle using a cell pressure probe. Measurements were made on the first four cell layers of the cortex, but no evidence of any diurnal fluctuation could be found. It was concluded that the conductance of membranes of endodermal and stelar cells may be responsible for the observed diurnal rhythm in root Lp(r). When mRNAs from roots were probed with cDNA from the Arabidopsis aquaporin AthPIP1a gene, an abundant transcript was found to vary in abundance diurnally under high-stringency conditions. The pattern of fluctuations resembled closely the diurnal pattern of variation in root Lp(r). The plasma membranes of root cells were found to contain an abundant hydrophobic protein with a molecular weight of about 31 kDa which cross-reacted strongly to an antibody raised against the evolutionarily conserved N-terminal amino acid sequence of AthPIP1a.

Journal Article↗
PubMed2006

Detection and transcript expression of S-RNase gene associated with self-incompatibility in apricot (Prunus armeniaca L.).

The identity and expression of S-RNase genotypes in the self-compatible (SC) apricot cultivar 'Katy' and the self-incompatible (SI) cultivar 'Xinshiji' were examined. We used allele specific polymerase chain reaction (AS-PCR) and designated the alleles in 'Katy' and 'Xinshiji' as S(8)Sc and S(9)S(10), respectively. The S-RNase gene was expressed in style at the balloon stage in both genotypes. Using real-time fluorescence quantification RT-PCR technology (FQRT-PCR), spatio-temporal expression patterns of S-RNase gene between 'Katy' and 'Xinshiji' were compared. The results revealed that the expression of the S-RNase gene in 'Katy' and 'Xinshiji' were different. The transcript abundance was distinctly diverse at the key stage (i.e., at 24 h after self-pollination) in both genotypes, and was greater in 'Xinshiji' (SI) than 'Katy' (SC). In addition, the abundance of the S-RNase transcript was higher in upper-half of style than in the lower-half of style or in the ovary. In the SI cultivar 'Xinshiji', the expression of S-RNase reminded a relatively high level after cross-pollination, but it dropped continuously after self-pollination and un-pollination.

Alleles↗
PubMed1989

Molecular probes for general testicular and specific spermatogenic function.

Northern analysis of human testis poly(A+) RNA with a mixture of oligonucleotide primer extended cDNA probes revealed several similar RNAs. These RNAs were subsequently cloned into a VPCS (vector-primer-cloner-sequencer) plasmid. One of these clones, NDHu1, was represented within the library a number of times and hybridized strongly to a poly(A+) RNA of congruent to 1.2 kb. Sequence analysis identified this clone as the URF 1 subunit of the mitochondrial NADH dehydrogenase (NDHu1). Comparison of the relative levels of the NDHu1 and human protamine 1 (HP1) transcripts revealed that HP1 was less abundant than NDHu1. This was unexpected, since it is known that within differentiating mammalian spermatid cells, protamine (HP1) is an abundant transcript. This suggested that the ratio of the relative levels of these two very different mRNAs was indicative of the relationship between specific spermatogenic function (germ cell transcription, determined by the level of the HP1 transcript) and general testicular cell function (determined by the level of the mitochondrial mRNAs, i.e. NDHu1). This correlation was maintained when several individuals expressing various degrees of testicular dysfunction were examined. This study suggests that these probes may be useful markers for general testicular and specific spermatogenic function.

Base Sequence↗
PubMed1995

Human steroidogenic acute regulatory protein: functional activity in COS-1 cells, tissue-specific expression, and mapping of the structural gene to 8p11.2 and a pseudogene to chromosome 13.

Steroidogenic acute regulatory protein (StAR) appears to mediate the rapid increase in pregnenolone synthesis stimulated by tropic hormones. cDNAs encoding StAR were isolated from a human adrenal cortex library. Human StAR, coexpressed in COS-1 cells with cytochrome P450scc and adrenodoxin, increased pregnenolone synthesis > 4-fold. A major StAR transcript of 1.6 kb and less abundant transcripts of 4.4 and 7.5 kb were detected in ovary and testis. Kidney had a lower amount of the 1.6-kb message. StAR mRNA was not detected in other tissues including placenta. Treatment of granulosa cells with 8-bromo-adenosine 3',5'-cyclic monophosphate for 24 hr increased StAR mRNA 3-fold or more. The structural gene encoding StAR was mapped using somatic cell hybrid mapping panels to chromosome 8p. Fluorescence in situ hybridization placed the StAR locus in the region 8p11.2. A StAR pseudogene was mapped to chromosome 13. We conclude that StAR expression is restricted to tissues that carry out mitochondrial sterol oxidations subject to acute regulation by cAMP and that StAR mRNA levels are regulated by cAMP.

Animals↗
PubMed1988

Upstream and downstream transcriptional control signals in the yeast retrotransposon, TY.

The yeast retrotransposon, Ty, shares many structural and functional features with retroviral proviruses. These include production of a terminally redundant major transcript. There are also two less abundant transcripts of 5.0 kb and 2.2 kb. Ty transcription is regulated by cell-type, that is it is reduced 5-20 fold in a/alpha diploids as compared to haploids. However control of expression of Ty is not well understood. By deletion analysis we have identified regions of the element which are involved in the activation and regulation of transcription. These signals are found both upstream and downstream of the mRNA start site. The downstream signals are within the region encoding the major Ty proteins. This organisation of transcriptional control signals is discussed with reference to the organisation of control signals in other yeast genes and in retroviral proviruses and other retro-elements.

Base Sequence↗
PubMed1992

Transcription patterns of human papillomavirus type 16 in genital intraepithelial neoplasia: evidence for promoter usage within the E7 open reading frame during epithelial differentiation.

Human papillomavirus (HPV) type 16 transcription was analysed by in situ hybridization using 125I-labelled subgenomic riboprobes, from 26 genital intraepithelial neoplastic (IN) lesions, in formalin-fixed biopsies from 18 different cases. Distinct transcription patterns separable by the presence or absence of late gene transcription were detected. In 12 lesions, late gene expression was absent; HPV transcripts corresponding to the E6 and E7 open reading frame (ORF) were detectable in all basal cells and were usually evenly distributed through all layers of the epithelium. Transcripts corresponding to the E1, E2 and E2/E4 ORFs were present in nine of 12 lesions and displayed a similar distribution. In 14 lesions late gene transcripts were present. E6 and E7 transcripts were detectable basally in all but one lesion. The levels of E7 but not E6 transcripts were markedly increased in the superficial cells of differentiating epithelia, with an identical distribution and at similar levels to those of the E2/E4 transcript. We propose that the most abundant transcript in genital IN lesions containing late gene expression is an E7/E1 [symbol: see text] E2/E4 transcript corresponding to that reported in HPV-6/11 condylomata and which is derived from a similar promoter within the E7 ORF.

Cell Transformation, Neoplastic↗
PubMed2004

Iron acquisition and regulation in Campylobacter jejuni.

Iron affects the physiology of bacteria in two different ways: as a micronutrient for bacterial growth and as a catalyst for the formation of hydroxyl radicals. In this study, we used DNA microarrays to identify the C. jejuni genes that have their transcript abundance affected by iron availability. The transcript levels of 647 genes were affected after the addition of iron to iron-limited C. jejuni cells. Several classes of affected genes were revealed within 15 min, including immediate-early response genes as well as those specific to iron acquisition and metabolism. In contrast, only 208 genes were differentially expressed during steady-state experiments comparing iron-rich and iron-limited growth conditions. As expected, genes annotated as being involved in either iron acquisition or oxidative stress defense were downregulated during both time course and steady-state experiments, while genes encoding proteins involved in energy metabolism were upregulated. Because the level of protein glycosylation increased with iron limitation, iron may modulate the level of C. jejuni virulence by affecting the degree of protein glycosylation. Since iron homeostasis has been shown to be Fur regulated in C. jejuni, an isogenic fur mutant was used to define the Fur regulon by transcriptome profiling. A total of 53 genes were Fur regulated, including many genes not previously associated with Fur regulation. A putative Fur binding consensus sequence was identified in the promoter region of most iron-repressed and Fur-regulated genes. Interestingly, a fur mutant was found to be significantly affected in its ability to colonize the gastrointestinal tract of chicks, highlighting the importance of iron homeostasis in vivo. Directed mutagenesis of other genes identified by the microarray analyses allowed the characterization of the ferric enterobactin receptor, previously named CfrA. Chick colonization assays indicated that mutants defective in enterobactin-mediated iron acquisition were unable to colonize the gastrointestinal tract. In addition, a mutation in a receptor (Cj0178) for an uncharacterized iron source also resulted in reduced colonization potential. Overall, this work documents the complex response of C. jejuni to iron availability, describes the genetic network between the Fur and iron regulons, and provides insight regarding the role of iron in C. jejuni colonization in vivo.

Adaptation, Physiological↗
PubMed1990

Characterization of an in vitro system for the synthesis of mRNA from human parainfluenza virus type 3.

A cell extract derived from human parainfluenza virus type 3-infected human lung carcinoma (HLC) cells synthesized mRNA in vitro. Under optimal conditions, the extract was able to support transcription of all virus-encoded genes as determined by hybridization analyses. The RNA products contained full-length poly(A)-containing mRNA species similar to those observed in acutely infected cells. Further purification of the viral nucleocapsids from the infected HLC cell extract resulted in total loss of the capacity of the extract to synthesize mRNA in vitro. However, the addition of cytoplasmic extracts from uninfected HLC cells to the nucleocapsid preparations restored transcription to levels observed in the infected cell lysates, indicating requirement of a host factor(s) in the human parainfluenza virus type 3 transcription process. In distinction to the abundant transcription observed in the cell extract from HLC cells, cell extract prepared from CV-1 cells failed to support transcription in vitro. High levels of RNase activity in the cell extract from CV-1 cells appears to be the principal reason for this difference.

Animals↗
PubMed1994

Riboprobe expression cassettes for measuring IGF-I, beta-actin and glyceraldehyde 3-phosphate dehydrogenase transcripts.

The development of riboprobe expression cassettes for phosphorimager-based quantitation of steady-state transcripts for three different genes using solution hybridization, RNase protection assays is described. Glyceraldehyde 3-phosphate dehydrogenase (GAPDH) and beta-actin genes are widely used as reporter genes to estimate the amount and integrity of RNA as well as for comparing gene expression among different tissues. To directly compare expression of these two genes in lymphoid tissue and liver, cDNA fragments of beta-actin and GAPDH from both mice and rats were generated by RT-PCR and cloned together into pGEM1 under control of the T7 RNA polymerase promoter. Antisense transcripts from this fusion construct protected the appropriate-sized fragments of beta-actin (115 nt) and GAPDH (214 nt) in RNA isolated from rat spleen, thymus and liver. Expression of GAPDH transcripts was less variable across tissues because this mRNA was only two-fold lower in liver as compared to either thymus or spleen, whereas expression of beta-actin transcripts was eight-fold lower in liver than in these tissues. Two other riboprobe expression cassettes (IGF-I/actin) were constructed by ligating a cDNA fragment of mouse or rat beta-actin that would protect 115 nt to either a mouse or rat IGF-I genomic DNA fragment containing 182 bp of exon 4. These mouse and rat IGF-I/actin riboprobes were used to conclusively demonstrate that rat CSF-1-derived bone marrow macrophages, mouse elicited peritoneal macrophages and the murine PU5-1R macrophage cell line synthesize abundant transcripts for both IGF-I and beta-actin. However, the mouse M1 progenitor myeloid cell line does not express RNA for IGF-I, as demonstrated by the absence of protected transcripts for IGF-I in the presence of abundant protected transcripts for beta-actin. Phosphorimager scanning of the gels revealed that macrophages of both mice and rats express IGF-I transcripts at a level of 60-100% of those found in liver. These data show that a single riboprobe can be developed to generate multigene antisense RNAs that can then be used to quantitatively compare IGF-I transcripts in macrophages and other tissues to an internal standard, with GAPDH transcripts being less variable among tissues than those for beta-actin. This approach should be broadly applicable for measuring a variety of markers of cellular activation.

Actins↗
PubMed1988

Regulation of multiple basic fibroblast growth factor messenger ribonucleic acid transcripts by protein kinase C activators.

The human astrocytoma cell line U87-MG expressed two major basic fibroblast growth factor (FGF) mRNA transcripts of 7.0 and 3.7 kilobase (kb), as well as several low abundance transcripts of lower mol wt (1.0-1.8 kb). The phorbol ester phorbol-12,13-dibutyrate caused a time- and dose-dependent increase in the abundance of basic FGF mRNA transcripts. At a concentration of 1 microM, phorbol ester increased the level of both the 7.0 and 3.7 kb transcripts within 4 h, reached a plateau at 1.5- to 2.5-fold above control levels by 6 h and remained elevated for at least 12 h. When measured at 6 h after drug addition, the abundance of both 7.0 and 3.7 kb transcripts was maximally stimulated by 100 nM phorbol ester (EC50 = 10-20 nM). FGF mRNA levels were also stimulated to a similar extent by platelet-derived growth factor (0.15-5 U/ml) or the synthetic diacylglycerol analog 1-oleoyl-2-acetyl-rac glycerol (1-300 nM) at doses which stimulated DNA synthesis in these cells. Neither (Bu)2cAMP (0.03-2 mM) nor A23187 (0.3-1000 nM) had any effect on FGF expression. When U87-MG cells were exposed to phorbol ester for 24 h several differences were observed: the dose response curve was shifted to the left (EC50 = 3-5 nM; maximum response at 10 nM phorbol ester) and the response of the 7.0 and 3.7 kb transcripts was attenuated at higher doses (100-1000 nM), perhaps reflecting down-regulation of protein kinase C by the phorbol ester.(ABSTRACT TRUNCATED AT 250 WORDS)

Astrocytoma↗
PubMed2004

The multiassembly problem: reconstructing multiple transcript isoforms from EST fragment mixtures.

Recent evidence of abundant transcript variation (e.g., alternative splicing, alternative initiation, alternative polyadenylation) in complex genomes indicates that cataloging the complete set of transcripts from an organism is an important project. One challenge is the fact that most high-throughput experimental methods for characterizing transcripts (such as EST sequencing) give highly detailed information about short fragments of transcripts or protein products, instead of a complete characterization of a full-length form. We analyze this "multiassembly problem"-reconstructing the most likely set of full-length isoform sequences from a mixture of EST fragment data-and present a graph-based algorithm for solving it. In a variety of tests, we demonstrate that this algorithm deals appropriately with coupling of distinct alternative splicing events, increasing fragmentation of the input data and different types of transcript variation (such as alternative splicing, initiation, polyadenylation, and intron retention). To test the method's performance on pure fragment (EST) data, we removed all mRNA sequences, and found it produced no errors in 40 cases tested. Using this algorithm, we have constructed an Alternatively Spliced Proteins database (ASP) from analysis of human expressed and genomic sequences, consisting of 13,384 protein isoforms of 4422 genes, yielding an average of 3.0 protein isoforms per gene.

Algorithms↗
PubMed2003

Accurate and statistically verified quantification of relative mRNA abundances using SYBR Green I and real-time RT-PCR.

Among the many methods currently available for quantifying mRNA transcript abundance, reverse transcription-polymerase chain reaction (RT-PCR) has proved to be the most sensitive. Recently, several protocols for real-time relative RT-PCR using the reporter dye SYBR Green I have appeared in the literature. In these methods, sample and control mRNA abundance is quantified relative to an internal reference RNA whose abundance is known not to change under the differing experimental conditions. We have developed new data analysis procedures for the two most promising of these methodologies and generated data appropriate to assess both the accuracy and precision of the two protocols. We demonstrate that while both methods produce results that are precise when 18S rRNA is used as an internal reference, only one of these methods produces consistently accurate results. We have used this latter system to show that mRNA abundances can be accurately measured and strongly correlate with cell surface protein and carbohydrate expression as assessed by flow cytometry under different conditions of B cell activation.

Animals↗
PubMed1996

Cloning and and characterization of hydrophobins-encoding cDNAs from the ectomycorrhizal basdiomycete Pisolithus tinctorius.

Major alterations of fungal gene expression are induced by the development of ectomycorrhiza, a symbiosis between tree roots and filamentous fungi. Several cDNAs corresponding to highly expressed transcripts of the Basidomycete Pisolithus tinctorius (Pt) were isolated from symbiotic tissues. Two of these abundant transcripts (hydPt-1 and hydPt-2) encoded polypeptides belonging to the hydrophobin (Hyd) family, a group of small cysteine-rich fungal proteins involved im morphogenesis and plant-fungus interactions. As shown for other Hyd, the hydPt-1 and hydPt-2 mRNAs were barely detectable in mycelium grown in liquid culture and highly accumulated in aerial hyphae. In addition, these transcripts were also abundant in eucalyptus globulus-Pt ectomycorrhiza in early stages of differentiation, during the colonisation of roots.

Amino Acid Sequence↗
PubMed1992

An in vitro system for studying the initial stages of cottontail rabbit papillomavirus infection.

Cottontail rabbit papillomavirus (CRPV) infection of an established cottontail epidermal cell line (Sf1Ep) resulted in the production of CRPV-specific transcripts without concomitant morphological transformation. The most abundant transcripts corresponded in size to those of the E6 and E7 open reading frames (ORFs), which are also among the commonest in domestic and cottontail rabbit papillomas. CRPV RNA production was both time- and dose-dependent, with RNA production diminishing with decreasing viral dose and increasing culture passage. Infected cultures contained episomal CRPV DNA, which did not appreciably change in abundance with time but was significantly reduced with culture passage. All features of in vitro infection, especially RNA production, were inhibited by CRPV-neutralizing, but not HPV-11-neutralizing, monoclonal antibodies. Much of this inhibition could be attributed to a blockage of viral penetration, as indicated by the reduction of CRPV DNA within virus-neutralized cultures. The results indicate that, although CRPV infection of Sf1Ep cells was abortive, it serves as a useful model for analysis of early infection events.

Animals↗
PubMed2001

Characterization of a human gene encoding nucleosomal binding protein NSBP1.

We characterize the cDNA and genomic structure of NSBP1, and demonstrate that it is a nuclear protein and the homologue of mouse Nsbp1, which is known to encode a nucleosomal binding and transcriptional activating protein related to the HMG-14/-17 chromosomal proteins. The encoded NSBP1 protein has 86% amino acid similarity to Nsbp1, including identity in nucleosomal binding domains of the HMG-14/-17 proteins. Our radiation hybrid data localize NSBP1 and Nsbp1 to homologous regions of chromosome X, with NSBP1 in Xq13.3 between DXS983 and DXS995 and Nsbp1 in the interval DXMit65 and DXMit39. Although Nsbp1 produces one mRNA transcript, NSBP1 produces three transcripts with alternate polyadenylated sites. The 3' untranslated region (UTR) of NSPB1 mRNA also contains several AU-rich elements (AREs), which are associated with rapid mRNA turnover. Northern analysis of NSBP1/Nsbp1 shows differences in transcript abundance among adult and fetal tissues, with predominant expression in liver, kidney, trabecular bone, and bone marrow stromal cells. However, a reverse transcriptase-PCR analysis shows nearly ubiquitous expression of the three NSBP1 transcripts in all tissues examined, although the abundance of each transcript was not quantified. NSBP1 is encoded by six exons and has exon-intron boundaries identical to the HMG-14/-17 genes. The last exon and the 3' UTR of NSBP1 contain retrotransposon sequences of HAL1, HERV-H, and L1MB7, suggesting that these retrotransposons were involved in the origin of NSPB1 from an ancestral-like HMG-14/-17 gene. The similarities among NSBP1, Nsbp1, and the HMG-14/-17 proteins suggest that NSBP1 may function as a nucleosomal binding and transcriptional activating element. Further, the AREs in the 3' UTR of NSPB1 suggest that alternate poly(A) site selection may mediate the mRNA stability of this gene.

3' Untranslated Regions↗