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PubMed1997

Differential Expression and Turnover of the Tomato Polyphenol Oxidase Gene Family during Vegetative and Reproductive Development.

Polyphenol oxidases (PPOs) are encoded by a highly conserved, seven-member gene family clustered within a 165-kb locus on chromosome 8 of tomato (Lycopersicon esculentum). Using gene-specific probes capable of differentiating between PPO A/C, PPO B, PPO D, and PPO E/F, we examined the spatial and temporal expression of this gene family during vegetative and reproductive development. RNA blots and in situ hybridization using these probes showed that although PPO expression is primarily confined to early stages of development, the steady-state mRNA levels of these genes are subject to complex patterns of spatial and temporal regulation in vegetative and reproductive organs. Young tomato leaves and flowers possess the most abundant PPO transcripts. PPO B is the most abundant in young leaves, whereas in the inflorescence PPO B and E/F transcripts are dominant. Differential expression of PPOs is also observed in various trichome types. PPO A/C are specifically expressed in type I and type IV trichomes. In contrast, PPO D is only expressed in type VI trichomes. Type I, IV, and VI trichomes possess PPO E/F transcripts. Immunolocalization verified the translational activity of PPOs identified by in situ hybridization and suggested cell-type-specific, developmentally programmed PPO turnover. In addition, immunolocalization demonstrated the accumulation of PPO in specific idioblast cells of stems, leaves, and fruits.

Journal Article↗
PubMed1991

Ubiquitin-encoding mRNA and mRNA recognized by genes encoding ubiquitin-conjugating enzymes are differentially expressed in division-synchronized cultures of Chlamydomonas reinhardtii.

Cells of Chlamydomonas reinhardtii were synchronized by a light/dark illumination cycle of 14:10 h. All cells divided within the first 2 h of the dark period, the synchronization index was calculated as 0.916. RNA was isolated every 2 h and hybridized to 32P-labeled probes encoding (i) ubiquitin from Chlamydomonas reinhardtii (UBM) and (ii) two different ubiquitin-conjugating enzymes from Saccharomyces cerevisiae (UBC2 and UBC3). Sequences with homology to yeast UBC2 and UBC3, which are required for sporulation/DNA repair and G1/S transition in yeast, respectively, were detected in C. reinhardtii. In the algae, the relative abundance of transcripts encoding ubiquitin fusion proteins and UBC2 homologues is most prominent at the end of the light phase and throughout the dark. The highest amount of a putative polyubiquitin encoding transcript was detected during the dark phase of the synchronized culture. A high amount of this transcript is also present during the 8th hour of the light phase which may imply that the transcription of polyubiquitin gene is not only restricted to stress conditions in C. reinhardtii. The relative abundance of transcripts with homology to UBC3 is most pronounced within the light period corresponding to G1 and S phases of the C. reinhardtii cell cycle.

Animals↗
PubMed2001

Analysis of intergenic spacer transcripts suggests 'read-around' transcription of the extrachromosomal circular rDNA in Euglena gracilis.

We report here the sequence of the 1743 bp intergenic spacer (IGS) that separates the 3'-end of the large subunit ribosomal RNA (rRNA) gene from the 5'-end of the small subunit (SSU) rRNA gene in the circular, extrachromosomal ribosomal DNA (rDNA) of Euglena gracilis. The IGS contains a 277 nt stretch of sequence that is related to a sequence found in ITS 1, an internal transcribed spacer between the SSU and 5.8S rRNA genes. Primer extension analysis of IGS transcripts identified three abundant reverse transcriptase stops that may be analogous to the transcription initiation site (TIS) and two processing sites (A' and A0) that are found in this region in other eukaryotes. Features that could influence processing at these sites include an imperfect palindrome near site A0 and a sequence near site A' that could potentially base pair with U3 small nucleolar RNA. Our identification of the TIS (verified by mung bean nuclease analysis) is considered tentative because we also detected low-abundance transcripts upstream of this site throughout the entire IGS. This result suggests the possibility of 'read-around' transcription, i.e. transcription that proceeds multiple times around the rDNA circle without termination.

Animals↗
PubMed1997

Cyclosporin A and FK506 reduce interleukin-5 mRNA abundance by inhibiting gene transcription.

The cytokine interleukin-5 (IL-5) selectively induces the proliferation, differentiation, and activation of mature eosinophils. The immunosuppressive agents cyclosporin A (CsA) and FK506 ameliorate the influx of eosinophils seen in allergic conditions such as asthma. We investigated the mechanisms controlling IL-5 messenger RNA (mRNA) expression in human T-lymphocytes in the presence of CsA or FK506. Fresh human peripheral blood mononuclear cells (PBMC); 7-day cultured PBMC, which represent a population of activated T-lymphocytes derived from PBMC; and the T-cell line HSB-2 were used. A novel polymerase chain reaction (PCR)-based nuclear run-on assay was employed to investigate the rate of IL-5 gene transcription. IL-5 mRNA degradation was measured by quantitative reverse transcriptase (RT)-PCR. CsA and FK506 strongly inhibited cellular IL-5 mRNA expression in response to phytohemagglutinin (PHA), or to phorbol myristate acetate (PMA), and/or calcium ionophore. Marked inhibition was observed in PBMC, 7-day cultured PBMC, and HSB-2 cells. Nuclear run-on assays done with either 7-day cultured PBMC or HSB-2 cells demonstrated striking inhibition of IL-5 gene transcription by both CsA and FK506 at levels reflecting the degree of reduction of total cellular IL-5 mRNA abundance. Neither CsA or FK506 had any detectable effect on the stability of IL-5 mRNA. Thus, the inhibitory effect of CsA and FK506 on cellular IL-5 mRNA expression can be explained by inhibition of the rate of IL-5 gene transcription.

Cells, Cultured↗
PubMed1979

Expression of the autonomous parvovirus H1 genome: evidence for a single transcriptional unit and multiple spliced polyadenylated transcripts.

We identified viral transcripts in parvovirus H1-infected rodent cells using the S1 nuclease mapping technique of Berk and Sharp (1977, 1978). The most abundant viral transcript, present in both nucleus and cytoplasm, is approximately 2.8 kb long and represents about 56% of the viral genome. Less abundant viral transcripts of 3.0, 1.45 and 1.30 kb, and possibly other minor viral transcripts, are also detected in nuclear and cytoplasmic fractions. In contrast, a prominent 4.7 kb viral transcript which corresponds to 95% of the viral DNA is found only in the nucleus; this finding suggests that the parvovirus genome may function as a single transcription unit. Virus-infected cells pretreated with cycloheximide accumulate all these viral transcripts. Analyses of RNA-DNA hybrids (isolated from neutral agarose gels) by electrophoresis on alkaline agarose gels indicate that the 4.7, 3.0 and 2.8 kb viral transcripts are "spliced" RNAs. The nuclear-specific 4.7 kb transcript appears to be encoded by two noncontiguous DNA segments of 2.2 and 2.6 kb. The 3.0 and 2.8 kb transcripts are apparently encoded by.a 2.6 kb segment of DNA and one or more much smaller noncontiguous DNA segments, one of which is approximately 170 nucleotides long.

Animals↗
PubMed1997

Differential expression of genes coding for ABC transporters after treatment of Arabidopsis thaliana with xenobiotics.

ATP-binding cassette (ABC) transporters are thought to be involved in many cellular detoxification mechanisms. Performing a BLAST search, we found four distinct expressed sequence tags (EST) of Arabidopsis thaliana highly similar to the human and fungal glutathione-conjugate ABC transporters. We studied the expression of the corresponding genes in response to various xenobiotics in an effort to gain information on their function. The abundance of transcripts corresponding to one of the genes (EST1) was not affected by the various compounds tested, whereas the abundance of transcripts corresponding to the other three genes (EST2, EST3, EST4) was increased by 1-chloro-2,4-dinitrobenzene, primisulfuron and IRL 1803. Treatment of Arabidopsis with either primisufuron or IRL 1803 resulted in a more than 40-fold increase in EST2-specific transcripts.

ATP-Binding Cassette Transporters↗
PubMed1972

Ribonucleic acid synthesis in cells infected with herpes simplex virus: controls of transcription and of RNA abundance.

Analysis of the kinetics of hybridization in liquid of labeled herpes simplex virus-1 DNA and excess viral RNA revealed the following: (i) Cells infected by herpes simplex virus-1 for 2 hr (before DNA synthesis) contain two classes of RNA molecules differing 140-fold in molar concentrations. The abundant and scarce RNAs are transcribed from 14 and 30% of the DNA, respectively. RNA extracted at 8 hr after infection (late RNA) also contains abundant and scarce classes differing 40-fold in molar concentrations; these are transcribed from 19 and 28% of viral DNA, respectively. Abundance competition hybridization tests indicate that the abundant RNA at 2 hr is a subset of the 8-hr abundant RNA. (ii) The abundant RNAs probably specify structural proteins, as indicated by estimates of DNA template required for structural proteins and by experiments showing that 19 of 24 proteins (corresponding to 68% of genetic information for structural proteins) are already made between 0.5 and 2 hr after infection. We conclude that there are two types of transcriptional controls, i.e., on-off and abundance controls, and that the synthesis of most structural components is an early viral function.

Amino Acids↗
PubMed2000

Cloning, modeling, and chromosomal localization for a small leucine-rich repeat proteoglycan (SLRP) family member expressed in human eye.

PURPOSE: To examine a highly abundant novel transcript from human iris. METHODS: Expressed sequence tag (EST) analysis of an adult human iris cDNA library revealed an abundant (>0.7%) transcript for a novel member of the small leucine-rich proteoglycan (SLRP) family. Other 3' ESTs from retina were also detected in dbEST. The structure of the leucine-rich repeat (LRR) domain was investigated by molecular modeling. Antisera were raised against a specific peptide and used in western blots of human and rat eye tissues. RESULTS: From its prevalence in the eye and its superfamily relationships, this SLRP protein has been given the names oculoglycan or opticin (Optc). Sequence analysis suggests that Optc has a signal peptide and two structural domains, the larger of which is the LRR domain. Modeling of the LRR domain reveals structural variability in the repeat motifs, forming potential interaction sites for binding partners. Antiserum to a specific peptide detected a protein of approximately 48 kDa, in human iris, ciliary body and retina while the major protein detected in rat ocular tissues was 37 kDa in size. This may reflect a species difference in post-translational modification. Radiation hybrid mapping shows that the gene for OPTC is located on chromosome 1q31, close to the inherited eye diseases ARMD1 and AXPC1. CONCLUSIONS: Optc is a newly identified SLRP family member, which appears to have eye-preferred expression. Molecular modeling reveals local deviations from the familiar LRR structure, which are candidates for specific interaction sites. Western blotting with a specific peptide antibody detects Optc in iris, ciliary body and retina in the human eye and suggests that the protein is post-translationally modified. In rat, the antibody detects Optc in several eye tissues and in brain but the protein appears to have undergone much less modification, suggesting that this is not essential for all aspects of function. Considering its eye-preferred expression, the OPTC gene has the potential for involvement in inherited eye disease. Indeed, it maps close to at least two disease loci for which no gene has so far been identified.

Adolescent↗
PubMed2000

Halocin S8: a 36-amino-acid microhalocin from the haloarchaeal strain S8a.

Halocin S8 is a hydrophobic microhalocin of 36 amino acids (3,580 Da) and is the first microhalocin to be described. This peptide antibiotic is unique since it is processed from inside a much larger, 33,962-Da pro-protein. Halocin S8 is quite robust, as it can be desalted, boiled, subjected to organic solvents, and stored at 4 degrees C for extended periods without losing activity. The complete amino acid sequence of halocin S8 was obtained first by Edman degradation of the purified protein and verified from the halS8 gene: H(2)N-S-D-C-N-I-N-S-N-T-A-A-D-V-I-L-C-F-N-Q-V-G-S-C-A-L-C-S-P-T-L-V-G -G-P-V-P-COOH. The halS8 gene is encoded on an approximately 200-kbp megaplasmid and contains a 933-bp open reading frame, of which 108 bp are occupied by halocin S8. Both the halS8 promoter and the "leaderless" halS8 transcript are typically haloarchaeal. Northern blot analysis revealed three halS8 transcripts: two abundant and one minor. Inspection of the 3' end of the gene showed only a single, weak termination site (5'-TTTAT-3'), suggesting that some processing of the larger transcripts may be involved. Expression of the halS8 gene is growth stage dependent: basal halS8 transcript levels are present in low concentrations during exponential growth but increase ninefold during the transition to stationary phase. Initially, halocin activity parallels halS8 transcript levels very closely. However, when halocin activity plateaus, transcripts remain abundant, suggesting inhibition of translation at this point. Once the culture enters stationary phase, transcripts rapidly return to basal levels.

Amino Acid Sequence↗
PubMed1989

Expression of viral and myelin gene transcripts in a murine CNS demyelinating disease caused by a coronavirus.

C57BI/6N mice develop a CNS demyelinating disease when inoculated intracranially at 4 weeks of age with the A59 strain of mouse hepatitis virus (MHV-A59). In order to explore the virus-host interactions, the histological features of the demyelinating disease were correlated with the spatial and temporal distribution of viral transcripts and the expression of oligodendrocyte-specific genes (myelin basic protein, proteolipid protein, myelin-associated glycoprotein, and 2',3' cyclic nucleotide 3'-phosphohydrolase) in the spinal cord of diseased mice. Three distinct phases in the disease were identified. In the first phase, 1 week postinfection (1 WPI), virus replication was widespread in both gray and white matter but was preferentially occurring in glial cells. In the ventral and dorsal root zones where viral transcripts were most abundant, all myelin gene transcripts were decreased before demyelination was seen. During the second phase of the disease (2-3 WPI), viral transcripts decreased in abundance and became restricted to the white matter. Numerous demyelinating lesions were observed and were characterized by inflammatory cells, paucity of oligodendrocytes, and a profound decrease of all myelin gene transcripts. In the third phase of the disease (4-6 WPI) no viral transcripts were detected, and remyelination began. In the lesions and the tissue surrounding them, transcripts of all myelin genes increased to levels above normal. The increased expression of myelin gene transcripts occurred in a synchronized manner and with a cellular distribution reminiscent of that seen in developmental myelination. These molecular events correlated with efficient remyelination and clinical recovery in this murine demyelinating disease.

Animals↗
PubMed2005

A RING domain gene is expressed in different cell types of leaf trace, stem, and juvenile bundles in the stem vascular system of zinnia.

The in vitro zinnia (Zinnia elegans) mesophyll cell system, in which leaf mesophyll cells are induced to transdifferentiate into tracheary elements with high synchrony, has become an established model for studying xylogenesis. The architecture of the stem vascular system of zinnia cv Envy contains three anatomically distinct vascular bundles at different stages of development. Juvenile vascular strands of the subapical region develop into mature vascular strands with leaf trace segments and stem segments. Characteristic patterns of gene expression in juvenile, leaf trace, and stem bundles are revealed by a molecular marker, a RING domain-encoding gene, ZeRH2.1, originally isolated from a zinnia cDNA library derived from differentiating in vitro cultures. Using RNA in situ hybridization, we show that ZeRH2.1 is expressed preferentially in two specific cell types in mature zinnia stems. In leaf trace bundles, ZeRH2.1 transcript is abundant in xylem parenchyma cells, while in stem bundles it is abundant in phloem companion cells. Both of these cell types show wall ingrowths characteristic of transfer cells. In addition, ZeRH2.1 transcript is abundant in some phloem cells of juvenile bundles and in leaf palisade parenchyma. The complex and developmentally regulated expression pattern of ZeRH2.1 reveals heterogeneity in the vascular anatomy of the zinnia stem. We discuss a potential function for this gene in intercellular transport processes.

Amino Acid Sequence↗
PubMed2001

Differential RNA expression of alpha-expansin gene family members in the parasitic angiosperm Triphysaria versicolor (Scrophulariaceae).

Haustoria are parasitic plant specific organs that locate, attach to, and invade host plant tissues. Parasitic species of the Scrophulariaceae develop haustoria on their roots in response to chemical signals released by host plant roots. Haustorium development was induced in vitro in roots of the parasitic Scrophulariaceae Triphysaria versicolor by treating them with exudates obtained from maize roots, the chemical 2,6-dimethoxybenzoquinone (DMBQ) or the cytokinin 6-benzylaminopurine (BAP). Morphological responses of T. versicolor roots to these haustoria inducing factors (HIFs) included localized swelling and epidermal hair proliferation near the root tips. These responses were not observed when roots of the non-parasitic Scrophulariaceae Lindenbergia muraria were similarly treated. Because expansin proteins are closely associated with plant cell wall expansion and growth, we examined the expression of expansin genes in response to HIFs. We isolated cDNAs homologous to transcripts encoding three distinct alpha-expansin proteins in T. versicolor. Northern-blot analyses indicated that these transcripts were differentially abundant in different tissues. Steady-state levels of two expansin transcripts increased in T. versicolor roots exposed to BAP, but not DMBQ or maize root exudates. Expansin transcript abundance also increased in L. muraria in response to BAP treatment. These results suggest that the expansins examined fulfill functions distinct from haustorium development.

Adenine↗
PubMed1988

Cloning, nucleotide sequence, and potential regulatory elements of the glutamine synthetase gene from murine 3T3-L1 adipocytes.

Glutamine synthetase [L-glutamate:ammonia ligase (ADP-forming); EC 6.3.1.2] specific activity, cellular content, mRNA abundance, and gene transcription rate increase by greater than 100-fold during adipocyte differentiation of 3T3-L1 cells. In 3T3-L1 adipocytes dexamethasone increases, whereas insulin as well as N6,O2'-dibutyryladenosine 3',5'-cyclic monophosphate decrease, glutamine synthetase gene expression. We analyzed the nucleotide sequence of a 1.9-kilobase Sal I-EcoRI restriction fragment from a 3T3-L1 glutamine synthetase genomic clone. This genomic fragment is composed of 1851 base pairs (bp) and includes the first exon and 1029 bp of the 5' flanking sequence. The 600 bp at the 3' end of the 1.9-kb Sal I-EcoRI restriction fragment constitute an open reading frame. We identified the transcription start site at a location 222 bp upstream of the glutamine synthetase coding sequences. The 5' flanking region of the gene encompasses several potential regulatory elements including TATA and CAAT sequences and a 40-bp poly(dT-dG).poly(dC-dA) putative enhancer element. Potential hormone and fat-specific regulatory elements are also located upstream of the transcription start site; they include glucocorticoid and cAMP response elements and fat-specific elements. These potential regulatory elements could account for the differentiation-associated changes and hormone-mediated changes seen in glutamine synthetase gene transcription and mRNA abundance.

Adipose Tissue↗
PubMed1991

Transcription of ribosomal DNA intergenic spacer sequences in normal and regenerating rat liver.

In regenerating rat liver both the transcriptional activity of the intergenic spacer rDNA promoter and the steady-state abundance of spacer transcripts are increased about 2-fold, as compared to normal liver. These changes are parallel to the observed 2.5-fold increase in regenerating liver of rRNA gene promotor activity and gene promotor transcripts abundance. These results suggest that both gene and spacer rDNA promotors are subject to common regulatory mechanisms. Our results indicate also that the stability of spacer transcripts in regenerating liver is not significantly altered.

Animals↗
PubMed1989

Globin gene expression in erythroid human fetal liver cells.

We measured steady-state levels of the human globin mRNAs in liver samples from several mid-gestational fetuses. RNA from the epsilon, gamma, beta, zeta, theta, and alpha globin genes were present in fetal liver samples isolated from 10-25-wk embryos. The abundance of all human globin mRNAs declined in older fetuses, presumably because of a gradual reduction in the proportion of erythroid precursors in the liver as development proceeds. The gamma:beta globin mRNA ratio in 10-18-wk fetal erythroblasts was 6-7:1, and in adult erythroid bone marrow the ratio was 0.02:1. In fetal liver samples, the relative abundance of epsilon transcripts was less than 1% that of gamma, and zeta transcripts less than 5% that of alpha. Embryonic transcripts declined in abundance during late fetal development and were not detected in newborn liver or adult erythroid bone marrow. theta globin mRNA also represented a minor species (less than 1% that of alpha) in fetal liver samples, but in contrast to the embryonic mRNAs, was most abundant in adult marrow samples obtained from patients with erythroid hyperplasia. These results support the hypothesis that globin protein levels are regulated by the relative amounts of each globin mRNA at various stages of erythropoietic development.

DNA Probes↗
PubMed1988

A Drosophila melanogaster G protein alpha subunit gene is expressed primarily in embryos and pupae.

A G protein alpha subunit gene has been isolated from a Drosophila melanogaster genomic library using a combination of bovine rod and cone transducin alpha subunit cDNAs as a probe under reduced stringency conditions. The gene, DG alpha 1, encodes a protein with an amino acid sequence 78% identical to bovine Gi alpha 1. However, unlike all reported Gi alpha subunit the DG alpha 1-encoded protein is not expected to be a pertussis toxin substrate, because it lacks a cysteine at the appropriate site. The protein coding region of the gene is split by four introns. The sequence of a head tissue cDNA clone, as well as amino acid similarities to mammalian G proteins, confirms this exon/intron structure. Northern blots of total cellular RNA reveal a major 2.3-kilobase transcript and a less abundant 1.7-kilobase transcript. These transcripts are most abundant in RNA from embryos and pupae. The DG alpha 1 gene is located on band 65C on the left arm of the third chromosome, on the basis of in situ hybridizations to Drosophila salivary gland polytene chromosomes.

Amino Acid Sequence↗
PubMed1984

Mapping and expression of a human cytomegalovirus major viral protein.

We constructed a DNA fragment map of low-passage Towne strain cytomegalovirus by analyzing cross-blot hybridization and hybridizations of isolated recombinant clones. The abundant late transcripts were located on this map by hybridization of labeled total RNA of virus-infected cells to blotted DNA fragments. The most abundant late transcript, carried by the 11.7-kilobase EcoRI fragment (EcoRI-G), was precisely mapped. The EcoRI fragment was fragmented and subcloned in a plasmid carrying simian virus 40 sequences (pSV-OH, constructed by Chi-Bom Chae, Department of Biochemistry, University of North Carolina, Chapel Hill). One resulting recombinant plasmid, pHD713SV2, was transferred to simian virus 40-transformed monkey kidney cells (COS-1) by DNA transfection. Synthesis of a cytomegalovirus-specific 67-kilodalton protein was detected in these cells by reaction of blotted proteins with virus-specific monoclonal antibody. The 67-kilodalton protein is a major phosphorylated protein found in virions; it is not glycosylated. The location of the gene for this 67-kilodalton protein is therefore assigned to the center of the L-unique region of human cytomegalovirus, at 0.37 to 0.39 map units.

Base Sequence↗
PubMed1995

Cholesterol side-chain cleavage cytochrome P450 gene expression in the primitive gut of the mouse embryo does not require steroidogenic factor 1.

In situ hybridization studies reveal novel sites of expression of cholesterol side-chain cleavage cytochrome P450 (P450scc) during murine embryonic development. In addition to fetal adrenals and testes, P450scc transcripts localize in situ to the primitive gut and to a subset of unidentified cells in the dermal mesenchyme of embryonic skin. In the gut, transcripts are most abundant in luminal epithelia of the hindgut, which will form the colon. P450scc transcript abundance at these novel sites is a fraction of that in fetal adrenals or testes, suggesting a local rather than an endocrine function. Immunocytochemical analyses localize P450scc protein to the fetal hindgut, indicating that the transcripts are translated in vivo. RNA isolated from microdissected embryonic hindgut and skin was reverse transcribed and amplified by polymerase chain reaction. DNA sequence analyses of polymerase chain reaction products confirmed that specific hybridization in situ represents authentic P450scc gene (Cyp11A) transcripts and that 3 beta-hydroxysteroid dehydrogenase/delta 5-->delta 4-isomerase transcripts are also present, demonstrating the potential of these fetal tissues to produce pregnenolone and progesterone. P450scc transcripts are also detectable by in situ hybridization in primitive gut and skin of Fushi tarazu factor 1 null mice, which lack the nuclear receptor steroidogenic factor 1, proving that steroidogenic factor 1 is not required for steroid hydroxylase gene expression at these sites. The capacity for C21 steroid biosynthesis in primitive gut and skin during organogenesis raises the question whether local production of steroid hormones may be required for normal cellular growth and differentiation of these tissues during embryogenesis.

Animals↗