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The auxin-induced K(+) channel gene Zmk1 in maize functions in coleoptile growth and is required for embryo development.

The transcript level and in turn protein density of the K(+)-uptake channel ZMK1 in maize (Zea mays) coleoptiles is controlled by the phytohormone auxin. ZMK1 is involved in auxin-regulated coleoptile elongation as well as gravi- and phototropism. To provide unequivocal evidence for the role of ZMK1 in these elementary processes we screened for maize plants containing a Mutator-tagged Zmk1 gene. In a site-selected approach, we were able to identify three independent alleles of Mutator-transposon insertions in Zmk1. zmk1-m1::Mu1 plants were characterised by a Mu1 transposon inside intron 1 of ZMK1. When we analysed the Zmk1-transcript abundance in growing coleoptiles of these homozygous mutants, however, we found the K(+)-channel allele overexpressed. In consequence, elevated levels of K(+)-channel transcripts resulted in a growth phenotype as expected from more efficient K(+)-uptake, representing a central factor for turgor formation. Following Zmk1 expression during maize embryogenesis, we found this K(+)-channel gene constitutively expressed throughout embryo development and upregulated in late stages. In line with a vital role in embryogenesis, the mutations of exon 2 and intron 2 of Zmk1-zmk1-m2::Mu8 and zmk1-m3::MuA2-caused a lethal, defective-kernel phenotype. Thus, these results demonstrate the central role of the auxin-regulated K(+)-channel gene Zmk1 in coleoptile growth and embryo development.

Alleles↗

The RNA polymerase II CTD kinase CTDK-I affects pre-mRNA 3' cleavage/polyadenylation through the processing component Pti1p.

There are several kinases in Saccharomyces cerevisiae that phosphorylate the CTD of RNA polymerase II, but specific and distinct functions of the phospho-CTDs generated by the different kinases are not well understood. A genetic screen for suppressors of loss of yeast CTD kinase I (CTDK-I) function (by deletion of the catalytic subunit gene CTK1) identified PTI1, a potential 3' cleavage/polyadenylation factor. Genetic and physical interactions connect Pti1p to components of CF IA and CF II/CPF, and mutations of PTI1 or CTK1 affect 3' cleavage site choice and transcript abundance of particular genes. Therefore, one important function of the CTDK-I-generated phospho-CTD appears to be the coupling of transcription to 3' processing of pre-mRNAs by a Pti1p-containing complex.

Amino Acid Sequence↗

An integrative genomics approach to infer causal associations between gene expression and disease.

A key goal of biomedical research is to elucidate the complex network of gene interactions underlying complex traits such as common human diseases. Here we detail a multistep procedure for identifying potential key drivers of complex traits that integrates DNA-variation and gene-expression data with other complex trait data in segregating mouse populations. Ordering gene expression traits relative to one another and relative to other complex traits is achieved by systematically testing whether variations in DNA that lead to variations in relative transcript abundances statistically support an independent, causative or reactive function relative to the complex traits under consideration. We show that this approach can predict transcriptional responses to single gene-perturbation experiments using gene-expression data in the context of a segregating mouse population. We also demonstrate the utility of this approach by identifying and experimentally validating the involvement of three new genes in susceptibility to obesity.

11-beta-Hydroxysteroid Dehydrogenase Type 1↗

NF-Y and CCAAT/enhancer-binding protein alpha synergistically activate the mouse amelogenin gene.

Amelogenin is the major protein component of the forming enamel matrix. In situ hybridization revealed a periodicity for amelogenin mRNA hybridization signals ranging from low to high transcript abundance on serial sections of developing mouse teeth. This in vivo observation led us to examine the amelogenin promoter for the activity of transcription factor(s) that account for this expression aspect of the regulation for the amelogenin gene. We have previously shown that CCAAT/enhancer-binding protein alpha (C/EBPalpha) is a potent transactivator of the mouse X-chromosomal amelogenin gene acting at the C/EBPalpha cis-element located in the -70/+52 minimal promoter. The minimal promoter contains a reversed CCAAT box (-58/-54) that is four base pairs downstream from the C/EBPalpha binding site. Similar to the C/EBPalpha binding site, the integrity of the reversed CCAAT box is also required for maintaining the activity of the basal promoter. We therefore focused on transcription factors that interact with the reversed CCAAT box. Using electrophoretic mobility shift assays we demonstrated that NF-Y was directly bound to this reversed CCAAT site. Co-transfection of C/EBPalpha and NF-Y synergistically increased the promoter activity. In contrast, increased expression of NF-Y alone had only marginal effects on the promoter. A dominant-negative DNA binding-deficient NF-Y mutant (NF-YAm29) dramatically decreased the promoter activity both in the absence or presence of exogenous expression of C/EBPalpha. We identified protein-protein interactions between C/EBPalpha and NF-Y by a co-immunoprecipitation analysis. These results suggest that C/EBPalpha and NF-Y synergistically activate the mouse amelogenin gene and can contribute to its physiological regulation during amelogenesis.

Amelogenin↗

Functional evidence for divergent receptor activation mechanisms of luteotrophic and luteolytic events in the human corpus luteum.

Using a dispersed human luteal cell culture model, progesterone synthesis following treatment by incremental doses of human chorionic gonadotrophin (HCG) and the stable prostaglandin F2alpha (PGF2alpha) analogue cloprostenol, alone or in combination, was related to corpora lutea (CL) mRNA transcript abundance coding for the luteinizing hormone (LH)/HCG receptor (LH-R) and PGF2alpha-receptor (FP) by semi-quantitative reverse transcription-polymerase chain reaction (RT-PCR) in 33 otherwise healthy women, scheduled for surgery due to benign conditions. CL were grouped according to age, based on the occurrence of a preovulatory LH surge where post-LH days 2-5 were designated as early luteal phase, days 6-10 as mid-luteal phase and days 11-14 as late luteal phase. When exposed to HCG, maximal progesterone output was raised 2.2-fold (P = 0.08, n = 5) compared with untreated controls in the early CL, while it increased 5.7- and 4.6-fold in the mid- and late groups respectively (P<0.05, n = 4 mid-luteal phase, n = 3 late luteal phase). This stimulation pattern was found to be concordant with the value of mRNA coding for LH-R in all groups (n = 6 early luteal phase, n = 5 mid-luteal phase, n = 6 late luteal phase). The integrated response to HCG and cloprostenol showed a dose-dependent 60% inhibition of progesterone production; but only in late luteal phase luteal cells (P<0.01, n = 3). FP mRNA values were lowest in early luteal phase, and increased with the age of the CL. Interestingly, lowest CL tissue concentrations of the natural FP agonist PGF2alpha were found during mid-luteal phase while it increased again 1.6-fold during late luteal phase (P<0.05, n = 8 versus mid-luteal phase, n = 6). Collectively, these data demonstrate that (i) the extrinsic functional control (or rescue of CL in the event of pregnancy) occurs when the sensitivity towards LH/HCG is maximal; and (ii) the demise of CL function is mediated via an acquisition of sensitivity towards the intrinsic luteolytic signal, PGF2alpha in the ageing CL.

Adult↗

Phototropin involvement in the expression of genes encoding chlorophyll and carotenoid biosynthesis enzymes and LHC apoproteins in Chlamydomonas reinhardtii.

Phototropin (PHOT) is a photoreceptor involved in a variety of blue-light-elicited physiological processes including phototropism, chloroplast movement and stomatal opening in plants. The work presented here tests whether PHOT is involved in expression of light-regulated genes in Chlamydomonas reinhardtii. When C. reinhardtii was transferred from the dark to very low-fluence rate white light, there was a substantial increase in the level of transcripts encoding glutamate-1-semialdehyde aminotransferase (GSAT), phytoene desaturase (PDS) and light-harvesting polypeptides (e.g. LHCBM6). Increased levels of these transcripts were also elicited by low-intensity blue light, and this blue-light stimulation was suppressed in three different RNAi strains that synthesize low levels of PHOT. The levels of GSAT and LHCBM6 transcripts also increased following exposure of algal cells to low-intensity red light (RL). The red-light-dependent increase in transcript abundance was not affected by the electron transport inhibitor 3-(3,4-dichlorophenyl)-1,1-dimethylurea, implying that the influence of RL on transcript accumulation was not controlled by cytoplasmic redox conditions, and that a red-light photoreceptor(s) may be involved in regulating the levels of transcripts from specific photosynthesis-related genes in C. reinhardtii. Interestingly, elevated GSAT and LHCBM6 transcript levels in RL were significantly reduced in the PHOT RNAi strains, which raises the possibility of co-action between blue and RL signaling pathways. Microarray experiments indicated that the levels of several transcripts for photosystem (PS) I and II polypeptides were also modulated by PHOT. These data suggest that, in C. reinhardtii, (i) PHOT is involved in blue-light-mediated changes in transcript accumulation, (ii) synchronization of the synthesis of chlorophylls (Chl), carotenoids, Chl-binding proteins and other components of the photosynthetic apparatus is achieved, at least in part, through PHOT-mediated signaling, and (iii) a red-light photoreceptor can also influence levels of certain transcripts associated with photosynthetic function, although its action requires normal levels of PHOT.

Algal Proteins↗

Expression of the endogenous Marek's disease virus ICP4 homolog (MDV ICP4) gene is enhanced in latently infected cells by transient transfection with the recombinant MDV ICP4 gene.

The ICP4 homolog of Marek's disease virus (MDV ICP4) is a possible candidate for the transactivator of the early genes. We transfected MDCC-MSB-1 (MSB-1) tumor cells with plasmid including a coding region of MDV ICP4 using cationic liposome. As carriers for intranuclear transport, high mobility group -1 and -2 proteins were bound to the plasmid DNA before forming liposomes. We detected transcripts from the plasmid 2 hr after transfection by quantitative reverse-transcriptase polymerase chain reaction (RT-PCR) analysis. We also detected abundant transcripts of endogenous ICP4 2-96 hr after transfection. These data suggested that expression of introduced MDV ICP4 gene enhanced the expression of endogenous MDV ICP4. On the other hand, quantitative PCR analysis for virus genome DNA indicated no significant alteration of copy number of virus genome in transfected MSB-1 cells, suggesting that reactivation of virus requires more than turning on MDV ICP4 gene.

Animals↗

Wood formation from the base to the crown in Pinus radiata: gradients of tracheid wall thickness, wood density, radial growth rate and gene expression.

Wood formation was investigated at five heights along the bole for two unrelated trees of Pinus radiata. Both trees showed clear gradients in wood properties from the base to the crown. Cambial cells at the base of the tree were dividing 3.3-fold slower than those at the crown, while the average thickness of cell walls in wood was highest at the base. Cell wall thickness showed an overall correlation coefficient of >0.7 with wood density in both genotypes. Microscopic examination of developing tracheids showed that 33% of cells had formed secondary cell walls at the base of the tree, reducing to 3% at the crown. In total, 455 genes differentially expressed in developing xylem tissue from either the base or the crown were identified using modified differential display. RT-PCR analysis of 156 genes confirmed differential expression for 77%. Of the genes tested, 73% showed gradients in transcript abundance either up or down the bole of the tree, although the steepness of the gradients differed between genes. Genes involved in cell division and expansion tended to be more highly expressed in the crown of the tree, and two putative cell-cycle repressor genes were expressed 2-fold higher at the base. Conversely, transcripts of genes involved in secondary wall thickening were more abundant at the base of the tree. These results suggest that differences in the rate of cambial cell division, differences in the rate and duration of tracheid wall thickening, and differences in gene expression underpin the gradients of wood properties found in pines.

Cell Wall↗

Coordinated genetic regulation of growth and lignin revealed by quantitative trait locus analysis of cDNA microarray data in an interspecific backcross of eucalyptus.

Phenotypic, genotypic, and transcript level (microarray) data from an interspecific backcross population of Eucalyptus grandis and Eucalyptus globulus were integrated to dissect the genetic and metabolic network underlying growth variation. Transcript abundance, measured for 2,608 genes in the differentiating xylem of a 91 (E. grandis x E. globulus) x E. grandis backcross progeny was correlated with diameter variation, revealing coordinated down-regulation of genes encoding enzymes of the lignin biosynthesis and associated methylation pathways in fast growing individuals. Lignin analysis of wood samples confirmed the content and quality predicted by the transcript levels measured on the microarrays. Quantitative trait locus (QTL) analysis of transcript levels of lignin-related genes showed that their mRNA abundance is regulated by two genetic loci, demonstrating coordinated genetic control over lignin biosynthesis. These two loci colocalize with QTLs for growth, suggesting that the same genomic regions are regulating growth, and lignin content and composition in the progeny. Genetic mapping of the lignin genes revealed that most of the key biosynthetic genes do not colocalize with growth and transcript level QTLs, with the exception of the locus encoding the enzyme S-adenosylmethionine synthase. This study illustrates the power of integrating quantitative analysis of gene expression data and genetic map information to discover genetic and metabolic networks regulating complex biological traits. (Sequence data for this article have been deposited with the EMBL/GenBank data libraries under accession numbers CB 967505 to CB 968059; CD 667988 to CD 670002; CD 670004; CD 670097; CD 670101 to CD 670112; and CD 670114 to CD 670137.)

Base Sequence↗

Serum leptin concentrations and expression of leptin transcripts in placental trophoblast with advancing baboon pregnancy.

Leptin is a polypeptide hormone originally thought to be produced exclusively by adipocytes. Recently, however, both leptin messenger ribonucleic acid (mRNA) and leptin protein were identified in human placental trophoblast cells, suggesting a potential role in primate pregnancy. In the present study, venous blood samples were collected at 5-day intervals during gestation from baboons (Papio sp), an established model for the study of human pregnancy, as well as from nonpregnant baboons, and leptin concentrations were determined by RIA. Additionally, placental villous tissue was collected upon cesarean delivery at early (days 60-62; n = 5), mid (days 98-102; n = 5), and late (days 159-167; n = 5) gestation (term = approximately 184 days), and leptin mRNA was quantitated by competitive RT-PCR. Finally, in situ hybridization was employed to localize transcripts to specific placental cell types. Results determined that maternal leptin levels (mean +/- SEM), which were dramatically greater (P<0.01) than those in nonpregnant cycling baboons (1.4+/-0.1 ng/mL), increased (P<0.005) with gestational age from 63.6+/-10.4 ng/mL on day 60 of gestation to 157.8+/-16.1 near term. Levels declined to those found in cycling baboons by 15 days postdelivery. In contrast to maternal leptin concentrations, placental leptin mRNA decreased (P<0.02) with advancing pregnancy, as transcript abundance declined approximately 8-fold from early to late gestation. Maternal peripheral leptin concentrations were positively correlated (r = 0.66; P<0.001) whereas placental leptin mRNA levels were negatively correlated (r = -0.64; P<0.01) with gestational age. Expression of leptin mRNA transcripts, as evidenced by RT-PCR in villous tissue, was localized principally within syncytiotrophoblast by in situ hybridization. In summary, changes in maternal peripheral leptin concentrations and placental leptin mRNA abundance that occur commensurate with advancing gestational age may imply evolving roles for the polypeptide with advancing primate pregnancy. In this capacity, localization of leptin transcripts within the baboon syncytiotrophoblast suggests the potential for autocrine or paracrine interactions within this endocrinologically active tissue. Finally, both the similarities in leptin ontogeny in baboon and human pregnancy and the singular enhancement of maternal leptin levels inherent throughout baboon gestation emphasize the potential of this nonhuman primate model for the study of leptin action in the maternal-fetoplacental unit.

Animals↗

Cloning and developmental expression in Xenopus laevis of seven additional members of the Wnt family.

Degenerate oligonucleotide primers encoding highly conserved regions of Wnt-related proteins were used with the polymerase chain reaction (PCR) to amplify cDNA derived from Xenopus laevis embryos. cDNA sequences partially encoding seven additional members of the Xwnt gene family were isolated using this strategy. These cDNAs have been given the designation Xwnt-2, Xwnt-6, Xwnt-7A, Xwnt-7B, Xwnt-7C, Xwnt-8B and Xwnt-10 based on their amino acid identity with previously described Wnts. With regard to the timing of expression of these Xwnts during embryonic development, Xwnt-2, the least abundant transcript, was first detected during the neurula stage, while Xwnt-8B transcripts were first detected at the gastrula stage, and decreased by the tailbud stage. Multiple transcripts of Xwnt-6 were detected at varied times during development beginning at the gastrula stage. In contrast, Xwnt-7A, -7B and -10 transcripts were not detected until the tailbud stage. With regard to expression in adult tissues, Xwnt-6, -7A, -7B, -8B and -10 were all expressed abundantly in the brain, and to a lesser extent in a variety of other tissues. Whole-mount in situ hybridization was then employed to monitor the spatial expression of selected Xwnts. Xwnt-7A and -10 transcripts were detected in distinct areas of the developing brain of tailbud-stage embryos. The temporal and spatial differences in expression suggest different roles for these new Xwnt family members in Xenopus development.

Amino Acid Sequence↗

Impacts of altered RNA metabolism on abscisic acid signaling.

The plant hormone abscisic acid (ABA) regulates many essential processes in growth and development. The recent characterization of ABA-sensitivity mutations in RNA-binding proteins has led to the recognition of a functional link between post-transcriptional mRNA processing and the ABA signal transduction machinery. By influencing transcript abundance, these RNA-binding proteins may modulate ABA signaling through the alteration of mRNA processing events such as splicing, 3' processing, nuclear export, transcript stability and RNA degradation.

Abscisic Acid↗

Completion of meiosis in Drosophila oocytes requires transcriptional control by grauzone, a new zinc finger protein.

Mutations in grauzone or cortex cause abnormal arrest in Drosophila female meiosis. We cloned grauzone and identified it as a C2H2-type zinc finger transcription factor. The grauzone transcript is present in ovaries and at later developmental stages. A Grauzone-GFP fusion protein is functional and localizes to nuclei of both nurse cells and follicle cells during oogenesis. Three lines of evidence indicate that grauzone and cortex interact: reducing cortex function enhanced the grauzone mutant phenotype; cortex transcript abundance is reduced in the absence of grauzone function and Grauzone protein binds to the cortex promoter. These results demonstrate that activation of cortex transcription by grauzone is necessary for the completion of meiosis in Drosophila oocytes, and establish a new pathway that specifically regulates the female meiotic cell cycle.

Alleles↗

Novel recombinations in the maize mitochondrial genome produce a unique transcriptional unit in the Texas male-sterile cytoplasm.

We have characterized a 3547 bp DNA fragment from male-sterile (cms-T) maize mitochondria, designated TURF 2H3, selected because of its unique and abundant transcripts. Sequence analysis indicated that TURF 2H3 originated by recombinations among portions of the flanking and/or coding regions of the maize mitochondrial 26S ribosomal gene, the ATPase subunit 6 gene, and the chloroplast tRNA-Arg gene. TURF 2H3 contains two long open reading frames that could encode polypeptides of 12,961 Mr and 24,675 Mr. The larger open reading frame hybridizes to transcripts in all maize cytoplasms, the smaller to transcripts only in T cytoplasm. TURF 2H3 transcripts appear to be uniquely altered in cms-T plants restored to fertility by the nuclear restorer genes Rf1 and Rf2. A possible relationship between TURF 2H3, nuclear restorer genes, and the male sterility trait in T cytoplasm is suggested.

Adenosine Triphosphatases↗

Differential response of Cu,Zn superoxide dismutases in two pea cultivars during a short-term exposure to sulfur dioxide.

Pea cultivars Progress and Nugget have been shown previously to be differentially sensitive with respect to apparent photosynthesis in a short-term exposure to 0.8 microliters/l SO2. One possible contributing factor to the relative insensitivity of apparent photosynthesis of Progress to SO2 is an increase in superoxide dismutase (SOD) activities. We show here that both chloroplastic and cytoplastic Cu,Zn-SOD proteins increased in Progress on exposure to sulfur dioxide whereas both proteins decreased in Nugget. The increase in cytosolic Cu,Zn-SOD protein was greater than that of chloroplastic Cu,Zn-SOD protein. Using a gene-specific probe for the plastid SOD, northern blot analysis revealed an initial decrease in transcript abundance of the chloroplastic Cu,Zn-SOD gene in Progress on exposure to SO2 with an eventual recovery to pre-exposure levels. The transcript levels of the chloroplastic Cu,Zn-SOD decreased in Nugget over the time period of the exposure. These results suggest that a combination of translational and post-translational mechanisms may be involved in SO2-induced changes in cytosolic and plastidic Cu,Zn-SODs in pea.

Chloroplasts↗

Localization of Epstein-Barr Virus-Encoded Small RNA-1 by in situ Reverse Transcription: Demonstration of cDNA Generation in Formalin-Fixed Paraffin-Embedded Tissue Sections.

Reverse transcription (RT) followed by polymerase chain reaction (RT-PCR) has been commonly used to detect viral and cellular transcripts in whole cell extracts. Application of this technique to tissue sections requires the in situ generation of cDNA. In this study, we selected an abundant transcript, Epstein-Barr virus (EBV)-encoded small RNA (EBER-1), as a model template to demonstrate cDNA generation in tissue sections. Using both digoxigenin-dUTP and primers which are complementary to EBER-1, we demonstrated specific EBER-1 cDNA generation both in vitro, and in tissue sections taken from formalin-fixed paraffin-embedded cell blocks of an EBV-infected cell line, B95-8. Furthermore, we utilized in situ RT in sections of EBV-associated nasopharyngeal carcinomas, and identified EBER-1 cDNA specifically in neoplastic cells, but not in the surrounding nonneoplastic stroma. EBER-1 cDNA was localized to the nucleus of these cells, with relative sparing of the nucleolus and the cytoplasm. No specific signal was evident if the reverse transcriptase was omitted, if 'sense' primers were used, or if RT was preceded by RNase digestion. The specificity of EBER-1 cDNA was further confirmed by in situ hybridization using the sense riboprobe, which has the same polarity as the EBER-1 transcript. Our results provide a successful example of using nonradioactive nucleotide analogue for cDNA generation in formalin-fixed, paraffin-embedded tissue sections. This approach would provide a visible assay to monitor RT in tissue sections, and allow further optimization of conditions for cDNA generation in tissue sections. Therefore, it potentially can be helpful for the future development of RT-PCR in tissue sections. Copyright 1995 S. Karger AG, Basel

Journal Article↗

Multiple mRNA species of choline acetyltransferase from rat spinal cord.

A cDNA library directed by a specific primer was constructed from the rat spinal cord and screened with 32P-labeled rat choline acetyltransferase cDNA which was recently isolated in this laboratory. Sequence analysis of 29 clones indicated that there are four types of cDNA (R1-, R2-, N1- and M-types). The nucleotide sequences in these cDNAs were identical in the coding region and the first 38 bp of the 5'-noncoding region, but differed in the 5'-noncoding region upstream of -38 bp. The R1-type was identical to the cDNA previously cloned from the rat spinal cord. The M and N1-type cDNAs both had sequences homologous to that of the cDNA previously obtained from the mouse spinal cord. Polymerase chain reaction analysis confirmed the presence of these 4 types of mRNA and found another type (N2-type) of transcript. The numbers of cDNA clones isolated and the relative amounts of polymerase chain reaction products for each type of mRNA suggested that the most abundant transcript was M-type. Sequencing of the genomic clone containing the 5'-region of choline acetyltransferase mRNA revealed that these five types of mRNA species were transcribed from three different promoter regions and produced by differential splicing of the 5'-noncoding exons.

Amino Acid Sequence↗

A mgl-like operon in Treponema pallidum, the syphilis spirochete.

A 38-kDa lipoprotein of Treponema pallidum subsp. pallidum (T. pallidum), the syphilis spirochete, previously was identified as a putative homolog of E. coli MglB [Becker et al. (1994) Infect. Immun. 62, 1381-1391]. In the present study, genome walking in regions adjacent to the T. pallidum 38-kDa lipoprotein gene has identified three contiguous genes (tp-mglB [formerly tpp38], tp-mglA, and tp-mglC) which appear to comprise a mgl-like operon in T. pallidum. A prominent transcript corresponding to tp-mglB, the first gene of the operon which encodes the carbohydrate receptor, is synthesized by T. pallidum along with lesser abundant transcript(s) corresponding to the entire T. pallidum mgl operon. An active promoter 135 bp upstream of tp-mglB is believed to direct mRNA synthesis for the operon. This is the first membrane protein-encoding operon of T. pallidum for which a putative function (glucose import) has been assigned. Furthermore, by analogy with E. coli MglB which interacts with the sensory transducer Trg to induce a chemotactic response, it is possible that T. pallidum also contains a homolog of E. coli Trg or other methyl-accepting chemotaxis proteins. The existence of a mgl operon in T. pallidum thus may have important implications with respect to T. pallidum survival, tissue dissemination, and sensory transduction during virulence expression.

Amino Acid Sequence↗