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Journal articles on the topic 'Transcript accumulation'

Author: Grafiati

Published: 4 June 2021

Last updated: 10 February 2022

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Boddu, Jayanand, Seungho Cho, Warren M. Kruger, and Gary J. Muehlbauer. "Transcriptome Analysis of the Barley-Fusarium graminearum Interaction." Molecular Plant-Microbe Interactions® 19, no. 4 (2006): 407–17. http://dx.doi.org/10.1094/mpmi-19-0407.

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Fusarium head blight (FHB) of barley (Hordeum vulgare L.) is caused by Fusarium graminearum. FHB causes yield losses and reduction in grain quality primarily due to the accumulation of trichothecene mycotoxins such as deoxynivalenol (DON). To develop an understanding of the barley-F. graminearum interaction, we examined the relationship among the infection process, DON concentration, and host transcript accumulation for 22,439 genes in spikes from the susceptible cv. Morex from 0 to 144 h after F. graminearum and water control inoculation. We detected 467 differentially accumulating barley gene transcripts in the F. graminearum-treated plants compared with the water control-treated plants. Functional annotation of the transcripts revealed a variety of infection-induced host genes encoding defense response proteins, oxidative burst-associated enzymes, and phenylpropanoid pathway enzymes. Of particular interest was the induction of transcripts encoding potential trichothecene catabolic enzymes and transporters, and the induction of the tryptophan biosynthetic and catabolic pathway enzymes. Our results define three stages of F. graminearum infection. An early stage, between 0 and 48 h after inoculation (hai), exhibited limited fungal development, low DON accumulation, and little change in the transcript accumulation status. An intermediate stage, between 48 and 96 hai, showed increased fungal development and active infection, higher DON accumulation, and increased transcript accumulation. A majority of the host gene transcripts were detected by 72 hai, suggesting that this is an important timepoint for the barley-F. graminearum interaction. A late stage also identified between 96 and 144 hai, exhibiting development of hyphal mats, high DON accumulation, and a reduction in the number of transcripts observed. Our study provides a baseline and hypothesis-generating dataset in barley during F. graminearum infection and in other grasses during pathogen infection.

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Jia, Haiyan, Seungho Cho, and Gary J. Muehlbauer. "Transcriptome Analysis of a Wheat Near-Isogenic Line Pair Carrying Fusarium Head Blight–Resistant and –Susceptible Alleles." Molecular Plant-Microbe Interactions® 22, no. 11 (2009): 1366–78. http://dx.doi.org/10.1094/mpmi-22-11-1366.

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Fusarium head blight (FHB), caused primarily by Fusarium graminearum, decreases grain yield and quality in wheat and barley. Disease severity, deoxynivalenol (DON), fungal biomass, and transcript accumulation were examined in a wheat near-isogenic line pair carrying either the resistant or susceptible allele for the chromosome 3BS FHB-resistance quantitative trait locus (Fhb1). Fhb1 restricts spread of disease symptoms but does not provide resistance to initial infection or initial DON accumulation. Wheat exhibits both induction and repression of large sets of gene transcripts during F. graminearum infection. In addition, a difference in the general timing of transcript accumulation in plants carrying either the resistant or susceptible allele at the Fhb1 locus was detected, and 14 wheat gene transcripts were detected that exhibited accumulation differences between the resistant and susceptible alleles. These results indicate that these may be host responses that differentiate the resistant from the susceptible interaction. Comparative analysis of the wheat–F. graminearum and the barley–F. graminearum interactions revealed a large set of conserved transcript accumulation patterns. However, we also detected gene transcripts that were repressed in wheat but not in barley. Based on the disease symptoms, transcript accumulation data, and comparative analysis of the barley and wheat host response to F. graminearum infection, we developed an integrated model for the interactions of wheat and barley with F. graminearum.

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Gunning, P., E. Hardeman, R. Wade, et al. "Differential patterns of transcript accumulation during human myogenesis." Molecular and Cellular Biology 7, no. 11 (1987): 4100–4114. http://dx.doi.org/10.1128/mcb.7.11.4100.

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We evaluated the extent to which muscle-specific genes display identical patterns of mRNA accumulation during human myogenesis. Cloned satellite cells isolated from adult human skeletal muscle were expanded in culture, and RNA was isolated from low- and high-confluence cells and from fusing cultures over a 15-day time course. The accumulation of over 20 different transcripts was compared in these samples with that in fetal and adult human skeletal muscle. The expression of carbonic anhydrase 3, myoglobin, HSP83, and mRNAs encoding eight unknown proteins were examined in human myogenic cultures. In general, the expression of most of the mRNAs was induced after fusion to form myotubes. However, several exceptions, including carbonic anhydrase and myoglobin, showed no detectable expression in early myotubes. Comparison of all transcripts demonstrated little, if any, identity of mRNA accumulation patterns. Similar variability was also seen for mRNAs which were also expressed in nonmuscle cells. Accumulation of mRNAs encoding alpha-skeletal, alpha-cardiac, beta- and gamma-actin, total myosin heavy chain, and alpha- and beta-tubulin also displayed discordant regulation, which has important implications for sarcomere assembly. Cardiac actin was the only muscle-specific transcript that was detected in low-confluency cells and was the major alpha-actin mRNA at all times in fusing cultures. Skeletal actin was transiently induced in fusing cultures and then reduced by an order of magnitude. Total myosin heavy-chain mRNA accumulation lagged behind that of alpha-actin. Whereas beta- and gamma-actin displayed a sharp decrease after initiation of fusion and thereafter did not change, alpha- and beta-tubulin were transiently induced to a high level during the time course in culture. We conclude that each gene may have its own unique determinants of transcript accumulation and that the phenotype of a muscle may not be determined so much by which genes are active or silent but rather by the extent to which their transcript levels are modulated. Finally, we observed that patterns of transcript accumulation established within the myotube cultures were consistent with the hypothesis that myoblasts isolated from adult tissue recapitulate a myogenic developmental program. However, we also detected a transient appearance of adult skeletal muscle-specific transcripts in high-confluence myoblast cultures. This indicates that the initial differentiation of these myoblasts may reflect a more complex process than simple recapitulation of development.

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Kaback, D. B., and L. R. Feldberg. "Saccharomyces cerevisiae exhibits a sporulation-specific temporal pattern of transcript accumulation." Molecular and Cellular Biology 5, no. 4 (1985): 751–61. http://dx.doi.org/10.1128/mcb.5.4.751.

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Cultures of the yeast Saccharomyces cerevisiae that are heterozygous for the mating type (MATa/MAT alpha) undergo synchronous meiosis and spore formation when starved for nitrogen and supplied with a nonfermentable carbon source such as acetate. Haploid and homozygous MAT alpha/MAT alpha and MATa/MATa diploid cells incubated under the same conditions fail to undergo meiosis and are asporogenous. It has not yet been firmly established that gene expression during sporulation is controlled at the level of transcript accumulation. To examine this question, we used cloned genes that encode a variety of "housekeeping" functions to probe Northern blots to assay the appearance of specific transcripts in both sporulating and asporogenous S. cerevisiae. In sporulating cells, each transcript showed a characteristic pattern of accumulation, reaching a maximum relative abundance at one of several different periods. In contrast, in both asporogenous haploid MATa and diploid MAT alpha/MAT alpha cells, all transcripts accumulated with similar kinetics. These results suggest a sporulation-specific pattern for transcript appearance. During these studies, high levels of several different transcripts were observed at unexpected times in sporulating cells. Histone (H)2A and (H)2B1 transcripts, although most abundant during premeiotic DNA synthesis, remained at one-third to one-half maximal levels after its end and were found in mature ascospores. Their appearance at this time is in sharp contrast to vegetative cells in which these histone transcripts are only found just before and during the period of DNA synthesis. Furthermore, transcripts from GAL10 and CDC10 genes, which are believed to be dispensable for sporulation, were much more abundant in sporulating cells than in asporogenous cells and vegetative cells grown on glucose or acetate. The presence of these transcripts did not appear to be due to a general activation of transcription because each accumulated with different kinetics. In addition, the transcript for at least one gene, HO, that is also dispensable for sporulation was not detected. The increased abundance of transcripts from some genes not required for sporulation leads us to propose that genes preferentially expressed during sporulation need not be essential for this differentiation.

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Hall, Jennifer R., Kathy A. Clow, Matthew L. Rise, and William R. Driedzic. "Identification and validation of differentially expressed transcripts in a hepatocyte model of cold-induced glycerol production in rainbow smelt (Osmerus mordax)." American Journal of Physiology-Regulatory, Integrative and Comparative Physiology 301, no. 4 (2011): R995—R1010. http://dx.doi.org/10.1152/ajpregu.00210.2011.

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Rainbow smelt ( Osmerus mordax ) avoid freezing by producing antifreeze protein (AFP) and accumulating glycerol. Glyceroneogenesis occurs in liver via a branch in glycolysis and gluconeogenesis and is activated by low temperature. Hepatocytes were isolated from the livers of fish acclimated to 8°C. Cells were incubated at warm (8°C; nonglycerol accumulating) or cold (0.4°C; glycerol accumulating) temperature over a 72-h time course. Reciprocal suppression subtractive hybridization libraries enriched for cold-responsive transcripts were constructed at 72 h. Microarray analyses using a 16K salmonid cDNA array were performed at 24, 48, and 72 h. Expression of type II AFP and 21 carbohydrate, amino acid, or lipid metabolism-related transcripts were validated using quantitative RT-PCR. Type II AFP transcript levels were not directly temperature related. In cold cells, levels of the glucose synthesis transcript were transiently higher. Increased glycerol production was not associated with increased phosphofructokinase or cytosolic glycerol-3-phosphate dehydrogenase transcript levels. Levels of transcripts (phosphoenolpyruvate carboxykinase, mitochondrial malate dehydrogenase, alanine aminotransferase, glutamate dehydrogenase, and aquaglyceroporin 9) associated with mobilization of amino acids to fuel glycerol accumulation were all transiently higher, suggesting a common regulatory mechanism. In cold compared with warm cells, pyruvate dehydrogenase kinase [an inhibitor of pyruvate dehydrogenase (PDH)] transcript levels were 20-fold higher. Potent inhibition of PDH would direct pyruvate and oxaloacetate derived from amino acids to glycerol, as opposed to oxidation via the citric acid cycle. Levels of a transcript potentially encoding glycerol-3-phosphatase, an enzyme not yet characterized in any vertebrate species, were higher following cold incubation. Finally, this study also presents the novel finding of increased glutamine synthetase transcript levels in response to low temperature.

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Raff, J. W., W. G. Whitfield, and D. M. Glover. "Two distinct mechanisms localise cyclin B transcripts in syncytial Drosophila embryos." Development 110, no. 4 (1990): 1249–61. http://dx.doi.org/10.1242/dev.110.4.1249.

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We demonstrate that two independent mechanisms act on maternally derived cyclin B transcripts to concentrate the transcripts at the posterior pole of the Drosophila oocyte and at the cortex of the syncytial embryo. The cortical accumulation occurs because the cyclin B transcript is concentrated around nuclei and comigrates with them to the cortex. The perinuclear localisation of the transcript is blocked by inhibitors of microtubule polymerisation and the transcript colocalises with microtubular structures during the cell cycle, suggesting that the transcript is associated either directly or indirectly with microtubules. Neither microtubules nor actin filaments are required to maintain the posterior concentration of cyclin B transcripts. Instead, this seems to depend on the association of the transcripts with a component of the posterior cytoplasm. The distribution pattern of the transcript at the posterior pole throughout embryogenesis and in a variety of mutant embryos suggests that this component is associated with polar granules.

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Wang, Xiao, Sameer P. Goregaoker, and James N. Culver. "Interaction of the Tobacco Mosaic Virus Replicase Protein with a NAC Domain Transcription Factor Is Associated with the Suppression of Systemic Host Defenses." Journal of Virology 83, no. 19 (2009): 9720–30. http://dx.doi.org/10.1128/jvi.00941-09.

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ABSTRACT An interaction between the helicase domain of the Tobacco mosaic virus (TMV) 126-/183-kDa replicase protein(s) and the Arabidopsis thaliana NAC domain transcription factor ATAF2 was identified via yeast two-hybrid and in planta immunoprecipitation assays. ATAF2 is transcriptionally induced in response to TMV infection, and its overexpression significantly reduces virus accumulation. Proteasome inhibition studies suggest that ATAF2 is targeted for degradation during virus infection. The transcriptional activity of known defense-associated marker genes PR1, PR2, and PDF1.2 significantly increase within transgenic plants overexpressing ATAF2. In contrast, these marker genes have reduced transcript levels in ATAF2 knockout or repressor plant lines. Thus, ATAF2 appears to function in the regulation of host basal defense responses. In response to TMV infections, ATAF2 and PR1 display increased transcript accumulations in inoculated tissues but not in systemically infected tissues. ATAF2 and PR1 transcript levels also increase in response to salicylic acid treatment. However, the salicylic acid treatment of systemically infected tissues did not produce a similar increase in either ATAF2 or PR1 transcripts, suggesting that host defense responses are attenuated during systemic virus invasion. Similarly, noninfected ATAF2 knockout or ATAF2 repressor lines display reduced levels of PR1 transcripts when treated with salicylic acid. Taken together, these findings suggest that the replicase-ATAF2 interaction suppresses basal host defenses as a means to promote systemic virus accumulation.

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Hann, Louane E., W. James Cook, Susan L. Uprichard, David M. Knipe, and Donald M. Coen. "The Role of Herpes Simplex Virus ICP27 in the Regulation of UL24 Gene Expression by Differential Polyadenylation." Journal of Virology 72, no. 10 (1998): 7709–14. http://dx.doi.org/10.1128/jvi.72.10.7709-7714.1998.

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ABSTRACT Herpes simplex virus specifies two sets of transcripts from theUL24 gene, short transcripts (e.g., 1.4 kb), processed at the UL24 poly(A) site, and long transcripts (e.g., 5.6 kb), processed at the UL26 poly(A) site. The 1.4- and 5.6-kb transcripts initiate from the same promoter but are expressed with early and late kinetics, respectively. Measurements of transcript levels following actinomycin D treatment of infected cells revealed that the 1.4- and 5.6-kb UL24 transcripts have similar stabilities, consistent with UL24 transcript kinetics being regulated by differential polyadenylation rather than by differential stabilities. Although the UL24 poly(A) site, which gives rise to short transcripts, is encountered first during processing, long transcripts processed at the UL26 site are equally or more abundant; thus, operationally, the UL24site is weak. Using a series of viral ICP27 mutants, we investigated whether ICP27, which has been suggested to stimulate the usage of weak poly(A) sites, stimulates 1.4-kb transcript accumulation. We found that accumulation of 1.4-kb transcripts did not require ICP27 during viral infection. Rather, ICP27 was required for full expression of 5.6-kb transcripts, and the decrease in 5.6-kb transcripts relative to 1.4-kb transcripts was not due solely to reduced DNA synthesis. Our results indicate that temporal expression of UL24transcripts can be regulated by differential polyadenylation and that although ICP27 is not required for processing at the operationally weakUL24 poly(A) site, it does modulate 5.6-kb transcript levels at a step subsequent to transcriptional initiation.

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Hu, Yan, Matt Plutz, and Andrew S. Belmont. "Hsp70 gene association with nuclear speckles is Hsp70 promoter specific." Journal of Cell Biology 191, no. 4 (2010): 711–19. http://dx.doi.org/10.1083/jcb.201004041.

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Many mammalian genes localize near nuclear speckles, nuclear bodies enriched in ribonucleic acid–processing factors. In this paper, we dissect cis-elements required for nuclear speckle association of the heat shock protein 70 (Hsp70) locus. We show that speckle association is a general property of Hsp70 bacterial artificial chromosome transgenes, independent of the chromosome integration site, and can be recapitulated using a 2.8-kilobase HSPA1A gene fragment. Association of Hsp70 transgenes and their transcripts with nuclear speckles is transcription dependent, independent of the transcribed sequence identity, but dependent on the Hsp70 promoter sequence. Transgene speckle association does not correlate with the amount of transcript accumulation, with large transgene arrays driven by different promoters showing no speckle association, but smaller Hsp70 transgene arrays with lower transcript accumulation showing high speckle association. Moreover, despite similar levels of transcript accumulation, Hsp70 transgene speckle association is observed after heat shock but not cadmium treatment. We suggest that certain promoters may direct specific chromatin and/or transcript ribonucleoprotein modifications, leading to nuclear speckle association.

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Chamot, Danuta, and George W. Owttrim. "Regulation of Cold Shock-Induced RNA Helicase Gene Expression in the Cyanobacterium Anabaena sp. Strain PCC 7120." Journal of Bacteriology 182, no. 5 (2000): 1251–56. http://dx.doi.org/10.1128/jb.182.5.1251-1256.2000.

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ABSTRACT Expression of the Anabaena sp. strain PCC 7120 RNA helicase gene crhC is induced by cold shock.crhC transcripts are not detectable at 30°C but accumulate at 20°C, and levels remain elevated for the duration of the cold stress. Light-derived metabolic capability, and not light per se, is required for crhC transcript accumulation. EnhancedcrhC mRNA stability contributes significantly to the accumulation of crhC transcripts, with the crhChalf-life increasing sixfold at 20°C. The accumulation is reversible, with the cells responding more rapidly to temperature downshifts than to upshifts, as a result of the lack of active mRNA destabilization and the continuation of crhC transcription, at least transiently, after a temperature upshift. Translational inhibitors do not induce crhC expression to cold shock levels, indicating that inhibition of translation is only one of the signals required to activate the cold shock response in Anabaena. Limited amounts of protein synthesis are required for the cold shock-induced accumulation of crhC transcripts, as normal levels of accumulation occur in the presence of tetracycline but are abolished by chloramphenicol. Regulation of crhC expression may also extend to the translational level, as CrhC protein levels do not correlate completely with the pattern of mRNA transcript accumulation. Our experiments indicate that the regulation of crhCtranscript accumulation is tightly controlled by both temperature and metabolic activity at the levels of transcription, mRNA stabilization, and translation.

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Fattash, Isam, Zachary Deitch, Relindis Njah, et al. "Accumulation Dynamics of Transcripts and Proteins of Cold-Responsive Genes in Fragaria vesca Genotypes of Differing Cold Tolerance." International Journal of Molecular Sciences 22, no. 11 (2021): 6124. http://dx.doi.org/10.3390/ijms22116124.

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Identifying and characterizing cold responsive genes in Fragaria vesca associated with or responsible for low temperature tolerance is a vital part of strawberry cultivar development. In this study we have investigated the transcript levels of eight genes, two dehydrin genes, three putative ABA-regulated genes, two cold–inducible CBF genes and the alcohol dehydrogenase gene, extracted from leaf and crown tissues of three F. vesca genotypes that vary in cold tolerance. Transcript levels of the CBF/DREB1 transcription factor FvCBF1E exhibited stronger cold up-regulation in comparison to FvCBF1B.1 in all genotypes. Transcripts of FvADH were highly up-regulated in both crown and leaf tissues from all three genotypes. In the ‘ALTA’ genotype, FvADH transcripts were significantly higher in leaf than crown tissues and more than 10 to 20-fold greater than in the less cold-tolerant ‘NCGR1363’ and ‘FDP817’ genotypes. FvGEM, containing the conserved ABRE promoter element, transcript was found to be cold-regulated in crowns. Direct comparison of the kinetics of transcript and protein accumulation of dehydrins was scrutinized. In all genotypes and organs, the changes of XERO2 transcript levels generally preceded protein changes, while levels of COR47 protein accumulation preceded the increases in COR47 RNA in ‘ALTA’ crowns.

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Doehlert, Douglas C., Leslie J. Smith, and Edwin R. Duke. "Gene expression during maize kernel development." Seed Science Research 4, no. 3 (1994): 299–305. http://dx.doi.org/10.1017/s0960258500002336.

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AbstractRelationships have been investigated between gene transcript abundance, enzyme activities and storage product accumulation in developing maize (Zea maysL.) kernels from 10 to 55 days postpollination (DPP). At the early stages of kernel development, there was very little increase in dry weight but kernels accumulated high concentrations of sugars and amino acids. At the end of this ‘lag’ phase (at 15 DPP), many transcripts appeared with little evidence of their translation. The initiation of the kernel-fill period at 20 DPP was characterized by a sudden rise in total RNA, increases in enzyme activities, and the initiation of storage product accumulation. Zein accumulation during this phase was highly correlated with α-zein transcript abundance. Starch accumulation was correlated with both the activity of ADP-GIc pyrophosphorylase and the abundance of gene transcripts encoding this enzyme (Shrunken-2andBrittle-2). DNA content of kernels increased linearly up to 30 DPP as a result of endoreplication, but had no apparent relationship to gene expression. DNA may accumulate as a storage product. Kernel-fill terminated when the moisture content fell below 36% and was marked by a decline of transcripts and a reduction of enzyme activities.

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Danckwardt, Sven, Gabriele Neu-Yilik, Rolf Thermann, Ute Frede, Matthias W. Hentze та Andreas E. Kulozik. "Abnormally spliced β-globin mRNAs: a single point mutation generates transcripts sensitive and insensitive to nonsense-mediated mRNA decay". Blood 99, № 5 (2002): 1811–16. http://dx.doi.org/10.1182/blood.v99.5.1811.

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Nonsense-mediated mRNA decay (NMD) represents a phylogenetically widely conserved splicing- and translation-dependent mechanism that eliminates transcripts with premature translation stop codons and suppresses the accumulation of C-terminally truncated peptides. Elimination of frameshifted transcripts that result from faulty splicing may be an important function of NMD. To test this hypothesis directly, this study used the IVS1 + 5 G&gt;A thalassemia mutation of the human β-globin gene as a model system. We generated β-globin gene constructs with this mutation and an iron-responsive element in the 5′ untranslated region, which allowed specific experimental activation and inactivation of translation and, hence, NMD of this transcript. Premessenger RNAs with IVS1 + 5 G&gt;A were spliced at normal sites and cryptic sites, enabling a direct comparison of the effect of NMD on the accumulation of normal and frameshifted messenger RNAs. In transfected HeLa cells, the predominant frameshifted transcript was degraded under conditions of active NMD, whereas accumulation to high levels occurred under conditions of specifically disabled NMD, thereby indicating an important physiologic function of NMD in the control of the splicing process. An unexpected finding was that accumulation of a second aberrant transcript remained unaffected by NMD. The IVS1 + 5 G&gt;A mutation thus revealed the presence of an unknown cis-acting determinant that influences the NMD sensitivity of a putative NMD substrate. It can therefore serve as a useful tool for defining the mechanisms that permit specific transcripts to circumvent the NMD pathway.

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Melčák, Ivo, Štěpánka Cermanová, Kateřina Jirsová, Karel Koberna, Jan Malı́nský, and Ivan Raška. "Nuclear pre-mRNA Compartmentalization: Trafficking of Released Transcripts to Splicing Factor Reservoirs." Molecular Biology of the Cell 11, no. 2 (2000): 497–510. http://dx.doi.org/10.1091/mbc.11.2.497.

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In the present study, the spatial organization of intron-containing pre-mRNAs of Epstein–Barr virus (EBV) genes relative to location of splicing factors is investigated. The intranuclear position of transcriptionally active EBV genes, as well as of nascent transcripts, is found to be random with respect to the speckled accumulations of splicing factors (SC35 domains) in Namalwa cells, arguing against the concept of the locus-specific organization of mRNA genes with respect to the speckles. Microclusters of splicing factors are, however, frequently superimposed on nascent transcript sites. The transcript environment is a dynamic structure consisting of both nascent and released transcripts, i.e., the track-like transcript environment. Both EBV sequences of the chromosome 1 homologue are usually associated with the track, are transcriptionally active, and exhibit in most cases a polar orientation. In contrast to nascent transcripts (in the form of spots), the association of a post-transcriptional pool of viral pre-mRNA (in the form of tracks) with speckles is not random and is further enhanced in transcriptionally silent cells when splicing factors are sequestered in enlarged accumulations. The transcript environment reflects the intranuclear transport of RNA from the sites of transcription to SC35 domains, as shown by concomitant mapping of DNA, RNA, and splicing factors. No clear vectorial intranuclear trafficking of transcripts from the site of synthesis toward the nuclear envelope for export into the cytoplasm is observed. Using Namalwa and Raji cell lines, a correlation between the level of viral gene transcription and splicing factor accumulation within the viral transcript environment has been observed. This supports a concept that the level of transcription can alter the spatial relationship among intron-containing genes, their transcripts, and speckles attributable to various levels of splicing factors recruited from splicing factor reservoirs. Electron microscopic in situ hybridization studies reveal that the released transcripts are directed toward reservoirs of splicing factors organized in clusters of interchromatin granules. Our results point to the bidirectional intranuclear movement of macromolecular complexes between intron-containing genes and splicing factor reservoirs: the recruitment of splicing factors to transcription sites and movement of released transcripts from DNA loci to reservoirs of splicing factors.

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Krause, Andrea, Vo T. T. Lan, and William J. Broughton. "Induction of Chalcone Synthase Expression by Rhizobia and Nod factors in Root Hairs and Roots." Molecular Plant-Microbe Interactions® 10, no. 3 (1997): 388–93. http://dx.doi.org/10.1094/mpmi.1997.10.3.388.

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Chalcone synthase (CHS) of Vigna unguiculata is encoded by a gene family that is abundantly transcribed in leaves and nodules. Inoculation with Rhizobium sp. NGR234, which nodulates V. unguiculata, or with NGRΔnodABC, a mutant deficient in Nod factor production, induced rapid accumulation of CHS mRNAs in roots and root hairs. As both Nod+ and Nod- bacteria provoke responses, induction of CHS gene expression may involve symbiotic or defense responses. Four days after inoculation with the wild-type Rhizobium sp., the transcript levels increased in roots but decreased in root hairs. Use of a region unique to the 5′ end of a specific CHS gene (VuCHS1) showed that increases of transcript levels in root hairs 24 h after inoculation with both rhizobia were specific to this gene. Transcripts of this gene in roots were only detectable 4 days after treatment with NGR234. It is possible therefore that accumulation of VuCHS1 follows the infection pathway of rhizobia entering legume roots. Purified Nod factors induced accumulation of transcripts, showing that they might be part of the signal transduction pathway leading to CHS expression.

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Gruszka, Damian, Ewa Pociecha, Barbara Jurczyk, et al. "Insights into Metabolic Reactions of Semi-Dwarf, Barley Brassinosteroid Mutants to Drought." International Journal of Molecular Sciences 21, no. 14 (2020): 5096. http://dx.doi.org/10.3390/ijms21145096.

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The roles of endogenous brassinosteroids (BRs) in the modulation of reaction to drought and genetic regulation of this process are still obscure. In this study, a multidirectional analysis was performed on semi-dwarf barley (Hordeum vulgare) Near-Isogenic Lines (NILs) and the reference cultivar “Bowman” to get insights into various aspects of metabolic reaction to drought. The NILs are defective in BR biosynthesis or signaling and displayed an enhanced tolerance to drought. The BR metabolism perturbations affected the glucose and fructose accumulation under the control and stress conditions. The BR metabolism abnormalities negatively affected the sucrose accumulation as well. However, during drought, the BR-deficient NILs accumulated higher contents of sucrose than the “Bowman” cultivar. Under the control conditions, accumulation of transcripts encoding antioxidant enzymes ascorbate peroxidase (HvAPX) and superoxide dismutase (HvSOD) was BR-dependent. However, during drought, the accumulation of HvAPX transcript was BR-dependent, whereas accumulations of transcripts encoding catalase (HvCAT) and HvSOD were not affected by the BR metabolism perturbations. The obtained results reveal a significant role of BRs in regulation of the HvAPX and HvCAT enzymatic activities under control conditions and the HvAPX and HvSOD activities during physiological reactions to drought.

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Peng, Weiping, Gail Henderson, Guey-Chuen Perng, Anthony B. Nesburn, Steven L. Wechsler, and Clinton Jones. "The Gene That Encodes the Herpes Simplex Virus Type 1 Latency-Associated Transcript Influences the Accumulation of Transcripts (Bcl-xL and Bcl-xS) That Encode Apoptotic Regulatory Proteins." Journal of Virology 77, no. 19 (2003): 10714–18. http://dx.doi.org/10.1128/jvi.77.19.10714-10718.2003.

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ABSTRACT The herpes simplex virus type 1 latency-associated transcript (LAT) inhibits apoptosis. We demonstrate here that LAT influences the accumulation of the Bcl-xL transcript versus the Bcl-xS transcript in Neuro-2A cells. Bcl-xL encodes an antiapoptotic protein, whereas Bcl-xS encodes a proapoptotic protein. Promoting the accumulation of Bcl-xL in neurons may inhibit apoptosis, thus enhancing the latency-reactivation cycle.

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Rabinow, L., S. L. Chiang, and J. A. Birchler. "Mutations at the Darkener of apricot locus modulate transcript levels of copia and copia-induced mutations in Drosophila melanogaster." Genetics 134, no. 4 (1993): 1175–85. http://dx.doi.org/10.1093/genetics/134.4.1175.

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Abstract Mutations of the Doa locus of Drosophila melanogaster darken the eye color of the copia-induced white(apricot) (wa) allele and increase the accumulation of white promoter-initiated transcripts encoding functional mRNA. We show here that quantities of transcripts initiated in both long terminal repeats (LTRs) of the specific wa-copia element are increased, and those initiating in the 5' LTR of the element are structurally altered, yielding a slightly shortened transcript. Accumulation of host-initiated transcripts of a copia-induced mutation within the achaete-scute complex, Hairy-wing Ua (HwUa), are reduced by Doa mutations. Finally, we show that homozygosity for Doa mutations increases the accumulation of copia transcripts from the population of elements in the genome. These results suggest that Doa modulates the severity of copia-induced mutations while functioning as a dosage-sensitive modulator of copia transcription.

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Dalby, B., and D. M. Glover. "3′ non-translated sequences in Drosophila cyclin B transcripts direct posterior pole accumulation late in oogenesis and peri-nuclear association in syncytial embryos." Development 115, no. 4 (1992): 989–97. http://dx.doi.org/10.1242/dev.115.4.989.

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We have characterised forms of the Drosophila cyclin B transcript that differ as a result of a splicing event which removes a nucleotide segment from the 3′ untranslated region. In oogenesis, both cyclin A RNA and a shorter form of the cyclin B transcript are seen in the cells of the germarium that are undergoing mitosis. The shorter cyclin B transcript alone is then detectable in the presumptive oocyte until stages 7–8 of oogenesis. Both cyclin A RNA and a longer form of the cyclin B RNA are then synthesised in the nurse cells during stages 9–11, to be deposited in the oocyte during stages 11–12. These transcripts become evenly distributed throughout the oocyte cytoplasm but, in addition, those of cyclin B become concentrated at the posterior pole. Examination of the distributions of RNAs transcribed from chimeric cyclin genes indicates that sequences in the 3′ untranslated region of the larger cyclin B RNA are required both for it to become concentrated at the posterior pole and to direct those transcripts in the body of the syncytial embryo to their peri-nuclear localisation. These sequences are disrupted by the splicing event which generates smaller cyclin B transcripts.

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Frick, K. K., P. J. Doherty, M. M. Gottesman, and C. D. Scher. "Regulation of the transcript for a lysosomal protein: evidence for a gene program modified by platelet-derived growth factor." Molecular and Cellular Biology 5, no. 10 (1985): 2582–89. http://dx.doi.org/10.1128/mcb.5.10.2582.

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Platelet-derived growth factor (PDGF) stimulates density-arrested BALB/c-3T3 cells to synthesize MEP, a lysosomal protein. This enhanced synthesis appears to be largely regulated by the PDGF-modulated accumulation of MEP mRNA, a 1.8-kilobase species. The increase in the MEP transcript, which is dependent on the PDGF concentration, begins 3 to 4 h after PDGF addition and is maximal at 12 h. The accumulation of the MEP transcript is growth-factor specific: PDGF and the tumor promoter 12-O-tetradecanoylphorbol-13-acetate, an agent which acts like PDGF, induce MEP RNA accumulation, whereas epidermal growth factor, somatomedin C, insulin, and whole plasma do not. A spontaneously transformed BALB/c-3T3 cell line (ST2-3T3), which does not require PDGF for growth, optimally expresses MEP RNA in the absence of PDGF. The PDGF-modulated increase in MEP RNA is unlike PDGF-modulated c-myc and c-fos RNA accumulation because it is blocked by cycloheximide, suggesting a requirement for de novo protein synthesis. It appears that PDGF modulates a program of gene expression with the accumulation of some transcripts, typified by MEP, being dependent upon the translation of others.

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Giannoulia, K., K. Haralampidis, Z. Poghosyan, D. J. Murphy, and P. Hatzopoulos. "Differential expression of diacylglycerol acyltransferase (DGAT) genes in olive tissues." Biochemical Society Transactions 28, no. 6 (2000): 695–97. http://dx.doi.org/10.1042/bst0280695.

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Fatty acids are accumulated in triacylglycerols (TAGs), in specialized organelles of seeds named oil bodies. The major site of TAG accumulation is detected in developing seed and mesocarp of certain species. We have isolated two cDNAs encoding DGAT enzymes from olives. The deduced polypeptides differ by 26 amino acids in size. However, they have high homology and almost identical hydropathy profiles. The DGAT gene is expressed in all tissues that synthesize TAGs. However, higher levels of DGAT transcripts have been detected in seed tissues of developing olive drupe. DGAT expression and mRNA accumulation in drupe tissues is developmentally regulated. Each DGAT transcript shows a distinct profile of accumulation. The existence of two different DGAT transcripts might reflect two different enzymes with discrete function and/or localization.

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Czékus, Zalán, Orsolya Csíkos, Attila Ördög, Irma Tari, and Péter Poór. "Effects of Jasmonic Acid in ER Stress and Unfolded Protein Response in Tomato Plants." Biomolecules 10, no. 7 (2020): 1031. http://dx.doi.org/10.3390/biom10071031.

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Endoplasmic reticulum (ER) stress elicits a protective mechanism called unfolded protein response (UPR) to maintain cellular homeostasis, which can be regulated by defence hormones. In this study, the physiological role of jasmonic acid (JA) in ER stress and UPR signalling has been investigated in intact leaves of tomato plants. Exogenous JA treatments not only induced the transcript accumulation of UPR marker gene SlBiP but also elevated transcript levels of SlIRE1 and SlbZIP60. By the application of JA signalling mutant jai1 plants, the role of JA in ER stress sensing and signalling was further investigated. Treatment with tunicamycin (Tm), the inhibitor of N-glycosylation of secreted glycoproteins, increased the transcript levels of SlBiP. Interestingly, SlIRE1a and SlIRE1b were significantly lower in jai1. In contrast, the transcript accumulation of Bax Inhibitor-1 (SlBI1) and SlbZIP60 was higher in jai1. To evaluate how a chemical chaperone modulates Tm-induced ER stress, plants were treated with sodium 4-phenylbutyrate, which also decreased the Tm-induced increase in SlBiP, SlIRE1a, and SlBI1 transcripts. In addition, it was found that changes in hydrogen peroxide content, proteasomal activity, and lipid peroxidation induced by Tm is regulated by JA, while nitric oxide was not involved in ER stress and UPR signalling in leaves of tomato.

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Rugkong, Adirek, Jocelyn K. C. Rose, and Chris B. Watkins. "GENE EXPRESSION AND ACTIVITIES OF CELL WALL-ASSOCIATED ENZYMES IN COLD-STORED TOMATO FRUIT." HortScience 41, no. 3 (2006): 494C—494. http://dx.doi.org/10.21273/hortsci.41.3.494c.

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Tomato fruit (Solanum lycopersicum L.) can develop mealiness and enhanced softening when exposed to chilling temperatures during storage, but the involvement of cell wall-associated enzymes in chilling injury development is not well understood. To study this aspect of injury development, we have exposed breaker-stage `Trust' tomato fruit to a chilling temperature of 3 °C for 0, 7, 14, and 21 days followed by storage at 20 °C for 12 days. Ethylene production was not affected by storage except after 21 days where production was greater at 20 °C. Exposure of fruit to chilling temperatures delayed the ripening-related color change (chroma and hue) and initially increased compression values, but percent extractable juice was not affected consistently. Increased polygalacturonase (PG) activity during ripening was reduced by about 50% after 7 days at 3 °C, and further inhibited with increasing storage periods. In contrast, the activities of pectin methylesterase (PME) and α-galactosidase were not significantly affected by the cold treatments. β-Galactosidase activity was greater in all chilled fruit compared with fruit ripened at harvest, whereas endo-β-1,4-glucanase activity was lower after 21 days at 3 °C. In chilled fruits, transcript accumulations for PG, PME (PME1.9), and expansin (Expt.1) were lower during storage at 20 °C compared with those of nonchilled fruits. Transcript accumulation for β-galactosidase (TBG4) was affected only at 14 days of cold storage, when transcript accumulation decreased. Cold treatment increased transcript accumulation of endo-β-1,4-glucanase (Cel1) after 12 days at 20 °C and decreased transcript accumulation after 7 days and 21 days at 21 °C. Cell wall analyses to investigate relationships among enzyme activities and cell wall disassembly are ongoing.

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Noya, Sara B., David Colameo, Franziska Brüning, et al. "The forebrain synaptic transcriptome is organized by clocks but its proteome is driven by sleep." Science 366, no. 6462 (2019): eaav2642. http://dx.doi.org/10.1126/science.aav2642.

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Neurons have adapted mechanisms to traffic RNA and protein into distant dendritic and axonal arbors. Taking a biochemical approach, we reveal that forebrain synaptic transcript accumulation shows overwhelmingly daily rhythms, with two-thirds of synaptic transcripts showing time-of-day–dependent abundance independent of oscillations in the soma. These transcripts formed two sharp temporal and functional clusters, with transcripts preceding dawn related to metabolism and translation and those anticipating dusk related to synaptic transmission. Characterization of the synaptic proteome around the clock demonstrates the functional relevance of temporal gating for synaptic processes and energy homeostasis. Unexpectedly, sleep deprivation completely abolished proteome but not transcript oscillations. Altogether, the emerging picture is one of a circadian anticipation of messenger RNA needs in the synapse followed by translation as demanded by sleep-wake cycles.

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Corbin, D. R., N. Sauer, and C. J. Lamb. "Differential regulation of a hydroxyproline-rich glycoprotein gene family in wounded and infected plants." Molecular and Cellular Biology 7, no. 12 (1987): 4337–44. http://dx.doi.org/10.1128/mcb.7.12.4337.

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We have characterized three different transcripts induced by fungal elicitor, wounding, or infection which encode apoproteins of cell wall hydroxyproline-rich glycoproteins involved in plant defense against infection. The proteins encoded by two of these transcripts contain a proline-rich domain involving tandem repetition of the 16-amino-acid unit Tyr3-Lys-Ser-Pro4-Ser-Pro-Ser-Pro4. The third transcript encodes a protein with a proline-rich domain involving a variant of this 16-mer canonical repeat: Tyr3-His-Ser-Pro4-Lys-His-Ser-Pro4. Each transcript is encoded by a separate gene present at single or low copy number in the haploid genome. These transcripts exhibit markedly different patterns of accumulation in different stress conditions, indicating the operation of several distinct intercellular stress signal systems in higher plants.

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Dill, Carren L., Roger P. Wise, and Patrick S. Schnable. "Rf8 and Rf* Mediate Unique T-urf13-Transcript Accumulation, Revealing a Conserved Motif Associated With RNA Processing and Restoration of Pollen Fertility in T-Cytoplasm Maize." Genetics 147, no. 3 (1997): 1367–79. http://dx.doi.org/10.1093/genetics/147.3.1367.

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Rf8 is a newly described nuclear gene that can substitute for Rf1 to partially restore pollen fertility to male-sterile, T-cytoplasm maize. Families segregating for Rf8 were used to investigate the mechanism of this fertility restoration and to compare it to the restoration conditioned by Rf1. Although Rf8 is unlinked to the rf1 locus, it also alters T-urf13 mitochondrial transcript accumulation and reduces the accumulation of the URF13 protein. Like the 1.6- and 0.6-kilobase (kb) T-urf13 transcripts that accumulate in T-cytoplasm plants carrying Rf1, 1.42- and 0.42-kb transcripts accumulate in plants that are partially restored by Rf8. A survey of T-cytoplasm maize lines, inbreds, and F1 hybrids by mitochondrial RNA gel blot analyses revealed that Rf8, is rare in maize germplasm. These surveys revealed the presence of another rare, weak restorer factor, Rf*, which is uniquely associated with the accumulation of 1.4- and 0.4-kb T-urf13 transcripts. Primer extension analyses position the 5′ termini of the 1.42/0.42-kb and 1.4/0.4-kb transcripts at +137 and +159 nucleotides, respectively, 3′ of the AUG initiation codon of the T-urf13 reading frame. The conserved motif, 5′-CNACNNU-3′, overlaps the 5′ termini of the Rf1-, Rf8-, and Rf*-associated transcripts and the 380 nucleotide, Rf3-associated orf107 transcript from cytoplasmic male sterility sorghum. These results demonstrate that multiple unlinked, nuclear genes can have similar but distinct effects on the expression of the unique T-urf13 mitochondrial coding sequence to restore pollen fertility to T-cytoplasm maize.

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Zhao, Tian-Yong, J. Willis Corum III, Jeffrey Mullen та ін. "An alkaline α-galactosidase transcript is present in maize seeds and cultured embryo cells, and accumulates during stress". Seed Science Research 16, № 2 (2006): 107–21. http://dx.doi.org/10.1079/ssr2006243.

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Raffinose family oligosaccharides (RFO) accumulate in many developing seeds and are degraded during seed germination. However, acidic α-galactosidase (AGAL) activity and subcellular location do not correlate with raffinose depletion; alkaline α-galactosidases (AGA) may be responsible for RFO hydrolysis in germinating seeds. Three cDNA clones for AGA/SEED IMBIBITION PROTEIN were obtained from the Pioneer Hi-Bred maize expressed sequence database. Two of the clones were expressed in Escherichia coli, and the recombinant proteins, when incubated with naturally occurring galactosides or p-nitrophenyl α-d-galactose, exhibited AGA activity with maximum catalysis at pH 7.5 (ZmAGA1) or pH 8.5 (ZmAGA3). No raffinose biosynthetic capacity was observed with either enzyme. Maximal α-galactosidase activity in mature dehydrated, germinating and germinated maize (Zea mays) seeds occurred at pH 7.5. ZmAGA1 was the sole family member detected in seeds and maize Hi-II, embryo-derived, callus cells. Its transcript accumulated when seed germination was interrupted by heat, cold or dehydration stress, but not in response to NaCl. Tissue prints localized transcripts to the scutellum or the embryo axis, depending on the stress applied. In maize Hi-II callus cells, transcripts accumulated when callus was subjected to heat stress (42 °C), during which ZmAGA1 transcript accumulation was further induced by sucrose. Galactosides in a variety of forms, including raffinose, partially repressed the sucrose-induced accumulation of transcript in heat-stressed callus.

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Ishov, Alexander M., Richard M. Stenberg, and Gerd G. Maul. "Human Cytomegalovirus Immediate Early Interaction with Host Nuclear Structures: Definition of an Immediate Transcript Environment." Journal of Cell Biology 138, no. 1 (1997): 5–16. http://dx.doi.org/10.1083/jcb.138.1.5.

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The development of an induced transcript environment was investigated at the supramolecular level through comparative localization of the human cytomegalovirus immediate early (IE) transcripts and specific nuclear domains shortly after infection. Compact aggregates of IE transcripts form only adjacent to nuclear domain 10 (ND10), and the viral protein IE86 accumulates exclusively juxtaposed to the subpopulation of ND10 with transcripts. The stream of transcripts is funneled from ND10 into the spliceosome assembly factor SC35 domain through the accumulation of IE86 protein, which recruits some components of the basal transcription machinery. Concomitantly the IE72 protein binds to ND10 and later disperses them. The domain containing the zinc finger region of IE72 is essential for this dispersal. Positional analysis of proteins IE86 and IE72, IE transcripts, ND10, the spliceosome assembly factor SC35, and basal transcription factors defines spatially and temporally an immediate transcript environment, the basic components of which exist in the cell before viral infection, providing the structural environment for the virus to usurp.

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Sawers, R. Gary. "Differential turnover of the multiple processed transcripts of the Escherichia coli focA-pflB operon." Microbiology 152, no. 8 (2006): 2197–205. http://dx.doi.org/10.1099/mic.0.28951-0.

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Expression of the anaerobically inducible focA-pflB operon of Escherichia coli is subject to complex transcriptional and post-transcriptional control, which generates eight transcripts whose 5′ ends span ∼1.2 kb. All eight transcripts have the same 3′ end. The 5′ ends of three of the transcripts, termed 6, 6a and 7, are located upstream of the operon. The promoters generating transcripts 6 and 7 are anaerobically regulated by FNR and ArcA∼P, while promoter 6a is constitutively active. The 5′ ends of the other five transcripts are all located within the operon. Most of the 5′ ends of these operon-internal transcripts result from RNA polymerase-dependent processing of the three longer primary transcripts, 6, 6a and 7. Here, it is demonstrated that subsequent to, and distinct from, these processing events, post-transcriptional modification of these transcripts also occurs through the action of the endoribonuclease RNase E. Transcripts 6 and 7 exhibit differential stability with half-lives of 1 and 5 min, respectively. Transcript 7, which has the longer half-life, is the longest transcript of the operon and has a ∼340 base untranslated leader. Two of the operon-internal transcripts, 4 and 5, also have comparatively short half-lives in the wild-type, which are significantly increased in a mutant with impaired RNase E activity. A precursor-product relationship is observed between the longer transcripts 3–7 and transcripts 1 and 2. The 5′ ends of transcripts 1 and 2 are closest to the pflB gene and have half-lives of approximately 7–8 min. The consequence of this regulation is an accumulation of full-length pflB transcript and comparably low levels of dicistronic transcript. This ensures different levels of synthesis of the formate transporter FocA and pyruvate formate-lyase during anaerobic growth, while maintaining coordinate regulation. Transcript analysis throughout the growth phase revealed that maximal anaerobic expression of the focA-pflB operon was restricted to exponentially growing cells. Expression of transcript 7 peaked in early to mid-exponential phase, while the levels of transcript 6 steadily accumulated toward the late-exponential phase of growth. Taken together, these findings indicate that although subject to common positive control by ArcA∼P and FNR, the transcripts generated by promoters 6 and 7 are subject to differential temporal and post-transcriptional regulation.

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Rosana, Albert Remus R., Denise S. Whitford, Anzhela Migur, et al. "RNA helicase–regulated processing of the Synechocystis rimO–crhR operon results in differential cistron expression and accumulation of two sRNAs." Journal of Biological Chemistry 295, no. 19 (2020): 6372–86. http://dx.doi.org/10.1074/jbc.ra120.013148.

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The arrangement of functionally-related genes in operons is a fundamental element of how genetic information is organized in prokaryotes. This organization ensures coordinated gene expression by co-transcription. Often, however, alternative genetic responses to specific stress conditions demand the discoordination of operon expression. During cold temperature stress, accumulation of the gene encoding the sole Asp–Glu–Ala–Asp (DEAD)-box RNA helicase in Synechocystis sp. PCC 6803, crhR (slr0083), increases 15-fold. Here, we show that crhR is expressed from a dicistronic operon with the methylthiotransferase rimO/miaB (slr0082) gene, followed by rapid processing of the operon transcript into two monocistronic mRNAs. This cleavage event is required for and results in destabilization of the rimO transcript. Results from secondary structure modeling and analysis of RNase E cleavage of the rimO–crhR transcript in vitro suggested that CrhR plays a role in enhancing the rate of the processing in an auto-regulatory manner. Moreover, two putative small RNAs are generated from additional processing, degradation, or both of the rimO transcript. These results suggest a role for the bacterial RNA helicase CrhR in RNase E-dependent mRNA processing in Synechocystis and expand the known range of organisms possessing small RNAs derived from processing of mRNA transcripts.

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Lilly, S. T., R. S. M. Drummond, M. N. Pearson, and R. M. MacDiarmid. "Identification and Validation of Reference Genes for Normalization of Transcripts from Virus-Infected Arabidopsis thaliana." Molecular Plant-Microbe Interactions® 24, no. 3 (2011): 294–304. http://dx.doi.org/10.1094/mpmi-10-10-0236.

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Real-time quantitative polymerase chain reaction (qPCR) of complementary DNA is now a standard method for studies of gene expression. However, qPCR can identify genuine variation only when transcript quantities are accurately normalized to an appropriate reference. To identify the most reliable reference genes for transcript quantification by qPCR, we describe a systematic evaluation of candidate reference genes of Arabidopsis thaliana ecotype Columbia-0 (Col-0). Twelve genes were selected for transcript stability studies by qPCR of complementary DNA prepared from Arabidopsis leaf tissue infected with one of five plant viruses (Cauliflower mosaic virus, Tobacco mosaic virus, Tomato spotted wilt virus, Turnip mosaic virus, and Turnip yellow mosaic virus). The F-box family protein, elongation factor 1-α, sand family protein, and protodermal factor 2 gene transcripts showed the most stable accumulation, whereas a traditionally used reference gene, Actin8, showed the least stable accumulation as measured by the geNorm algorithm. The data furnish plant virologists with reference genes for normalization of qPCR-derived gene expression in virus-infected Arabidopsis and will be beneficial to the selection and design of primers targeting orthologous genes in other plant species.

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Banik, Mitali, Scott Duguid, and Sylvie Cloutier. "Transcript profiling and gene characterization of three fatty acid desaturase genes in high, moderate, and low linolenic acid genotypes of flax (Linum usitatissimum L.) and their role in linolenic acid accumulation." Genome 54, no. 6 (2011): 471–83. http://dx.doi.org/10.1139/g11-013.

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Three genes encoding fatty acid desaturase 3 (fad3a, fad3b, and a novel fad3c) were cloned from four flax genotypes varying in linolenic acid content. Real-time PCR was used to quantify expression levels of the three fad3 genes during seed development. High amounts of both fad3a and fad3b transcripts were observed and reached their peak levels at 20 days after anthesis, except for fad3a from SP2047 where only low level expression was observed throughout seed development. Transcript accumulation of the novel fad3c gene was at similar background levels. The fatty acid composition was analysed for all genotypes and stages of development and compared with the fad3 gene expression patterns. α-Linolenic acid gradually accumulated during seed development, while linoleic acid was transient and decreased in M5791, UGG5-5, and AC McDuff. In contrast, the linolenic acid present in the early stages of development nearly completely disappeared in SP2047, while linoleic acid steadily accumulated. fad3a of the low linolenic acid line SP2047 encoded a truncated protein caused by a premature stop codon resulting from a single point mutation, and the low level of transcript accumulation in this genotype is likely due to nonsense-mediated mRNA decay caused by the premature termination of translation as a result of this early stop codon. Although substantial amounts of transcript accumulation occurred with fad3b of SP2047 genotype, cloning of the gene revealed a mutation in the first histidine box causing an amino acid change. Heterologous expression in yeast of the SP2047 and UGG5-5 fad3b genes showed that the mutation in the histidine box in SP2047 caused the enzyme inactivity. Taken together, these results showed that fad3a and fad3b are responsible for linolenic acid accumulation in flax seeds but did not support a major role for the novel fad3c. These observations were further supported by phenotypic and genotypic assessment of a doubled haploid population. Expression patterns of fad3a and fad3b were highly correlated with linolenic acid accumulation during seed development, with the exception of fad3b in SP2047 whose lack of activity was caused by the histidine box mutation despite its transcript accumulation being similar to that of the fad3b of the other genotypes.

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Muzzalupo, Innocenzo, Barbara Macchione, Cristina Bucci, et al. "LOXGene Transcript Accumulation in Olive (Olea europaeaL.) Fruits at Different Stages of Maturation: Relationship between Volatile Compounds, Environmental Factors, and Technological Treatments for Oil Extraction." Scientific World Journal 2012 (2012): 1–9. http://dx.doi.org/10.1100/2012/532179.

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The quality of olive oil is influenced by genetic and environmental factors and by the maturation state of drupes, but it is equally affected by technological treatments of the process. This work investigates the possible correlation between oliveLOXgene transcript accumulation, evaluated in fruits collected at different stages of maturation, and chemical biomarkers of its activity. During olive fruit ripening, the same genotype harvested from two different farms shows a positive linear trend betweenLOXrelative transcript accumulation and the content of volatile compounds present in the olive oil aroma. Interestingly, a negative linear trend was observed betweenLOXrelative transcript accumulation and the content of volatile compounds present in the olive pastes obtained from olive fruits with and without malaxation. The changes in the oliveLOXtranscript accumulation reveal its environmental regulation and suggest differential physiological functions for the LOXs.

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Mahmood, Riaz, Jane C. Hines, and Dan S. Ray. "Identification of cis andtrans Elements Involved in the Cell Cycle Regulation of Multiple Genes in Crithidia fasciculata." Molecular and Cellular Biology 19, no. 9 (1999): 6174–82. http://dx.doi.org/10.1128/mcb.19.9.6174.

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ABSTRACT Transcripts of several DNA replication genes, including theRPA1 and TOP2 genes, encoding the large subunit of nuclear replication protein A and the kinetoplast topoisomerase II, accumulate periodically during the cell cycle in the trypanosomatidCrithidia fasciculata. An octamer consensus sequence, CAUAGAAG, present in the 5′ untranslated regions (UTR) of these mRNAs is required for periodic accumulation of the TOP2 andRPA1 transcripts and also for binding of a nuclear factor(s) to the 5′ UTR RNAs of these genes. We show here that insertion of multiple (six) copies of this octamer sequence (6× octamer) into the 5′ UTR of a reporter gene confers periodic accumulation on its transcript. Competition experiments and UV cross-linking studies show that the 6× octamer RNA andTOP2 5′ UTR RNA bind to the same nuclear factor(s). Single-nucleotide substitutions in the 6× octamer that abolish the RNA gel shift also prevent cyclic accumulation of the reporter gene transcript. A protein termed cycling element binding protein, purified by affinity chromatography using 6× octamer RNA as a ligand, binds to RNAs containing wild-type octamers and not to those with mutant octamers. These results define a small sequence element in C. fasciculata mRNAs required for their cell cycle regulation and report the identification and purification of a putative regulatory protein that binds specifically to these elements.

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Treger, J. M., K. A. Heichman, and K. McEntee. "Expression of the yeast UB14 gene increases in response to DNA-damaging agents and in meiosis." Molecular and Cellular Biology 8, no. 3 (1988): 1132–36. http://dx.doi.org/10.1128/mcb.8.3.1132.

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The polyubiquitin gene, UB14, of Saccharomyces cerevisiae is regulated by a variety of environmental stresses and physiological conditions. After exposure of rapidly growing yeast cells to DNA-damaging agents (4-nitroquinoline-1-oxide and N-methyl-N'-nitro-N-nitrosoguanidine), intracellular levels of UB14 transcript increased rapidly. Induction of UB14 transcripts occurred within 30 to 60 min of exposure to 4-nitroquinoline-1-oxide in RAD+, rad52, and rad6 repair-deficient yeast strains. In high-density RAD+ cultures, the effect of alkylating agents on UB14 transcript levels is attenuated, in part because of significant increases in the basal level of this message in untreated cells. We also observed that the levels of UB14 transcripts increased significantly when diploid cells were exposed to sporulation conditions. Maximal levels of UB14 transcripts were reached after 6 to 8 h in sporulation medium. Accumulation of UB14 transcripts occurred in a/alpha diploids that undergo meiosis but not in asporogenous alpha/alpha diploids exposed to the same nutritional conditions.

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Ellison, Kimberly S., Stephen A. Rice, Robert Verity та James R. Smiley. "Processing of α-Globin and ICP0 mRNA in Cells Infected with Herpes Simplex Virus Type 1 ICP27 Mutants". Journal of Virology 74, № 16 (2000): 7307–19. http://dx.doi.org/10.1128/jvi.74.16.7307-7319.2000.

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ABSTRACT Herpes simplex virus (HSV) ICP27 is an essential and multifunctional regulator of viral gene expression that modulates RNA splicing, polyadenylation, and nuclear export. We have previously reported that ICP27 causes the cytoplasmic accumulation of unspliced α-globin pre-mRNA. Here we examined the effects of a series of ICP27 mutations that alter important functional regions of the protein on the processing and nuclear transport of α-globin and HSV ICP0 RNA. The results demonstrate that ICP27 mutants that are impaired for growth in noncomplementing cells, including mutants in the N- and C-terminal regions, are defective in the accumulation of α-globin pre-mRNA. Unexpectedly, several mutants that are competent to repress the expression of reporter genes in transient transfection assays failed to accumulate unspliced RNA, implying that different mechanisms are responsible for transrepression and pre-mRNA accumulation. Several mutants caused a marked increase in the length and heterogeneity of the α-globin mRNA poly(A) tail, suggesting that ICP27 may directly or indirectly affect the regulation of poly(A) polymerase. ICP27 was also required for the accumulation of multiple ICP0 intron-bearing transcripts, but this effect displayed a mutational sensitivity profile different from that of accumulation of unspliced α-globin RNA. Moreover, unlike spliced and unspliced α-globin RNAs, which were efficiently exported to the cytoplasm, spliced and intron-containing ICP0 transcripts were predominantly nuclear in localization, and ICP27 was not required for nuclear retention of the spliced message. We propose that these transcript- and ICP27 allele-specific differences may be explained by the presence of a strong cis-acting ICP27 response element in the α-globin transcript.

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Chica, Eduardo J., and L. Gene Albrigo. "Changes in CsFT Transcript Abundance at the Onset of Low-temperature Floral Induction in Sweet Orange." Journal of the American Society for Horticultural Science 138, no. 3 (2013): 184–89. http://dx.doi.org/10.21273/jashs.138.3.184.

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As in arabidopsis (Arabidopsis thaliana), putative citrus (Citrus) Flowering locus T (FT) homologs are strong promoters of flowering and apparently are key components of the molecular mechanism controlling floral induction in these species. An abundance of citrus FT gene transcripts during floral induction is consistent with the role of their products as floral-promoting signals. However, specific details about how the floral induction process is initiated and sustained remain largely unknown. We report changes in transcript abundance of a FT gene (CsFT) from sweet orange (Citrus sinensis) at the onset of floral induction by low temperatures and at different times of the day. Using a combination of field and growth room experiments, we determined that the abundance of CsFT transcripts increased within 1 day after initial exposure to cool floral-inductive temperatures, and that CsFT transcript abundance was higher in the afternoon than in the morning and evening. The presence of photoperiod cycles seemed to be required to sustain the increasing CsFT transcript abundance, because exposure to floral inductive conditions under continuous light or darkness did not increase the abundance of CsFT transcripts after 3 days. Our results suggest that the regulation of CsFT expression responds rapidly (overnight) to the onset of floral-inductive cool temperatures, is sensitive to changes in temperature, and requires alternation of light and dark cycles to sustain transcript accumulation during induction.

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Danilova, M. N., A. S. Doroshenko, D. A. Zabrodin, N. V. Kudryakova, R. Oelmüller, and V. V. Kusnetsov. "Cytokinin membrane receptors modulate transcript accumulation of plastid encoded genes." Russian Journal of Plant Physiology 64, no. 3 (2017): 301–9. http://dx.doi.org/10.1134/s1021443717030062.

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Savada, Raghavendra P., and Peta C. Bonham-Smith. "Differential transcript accumulation and subcellular localization of Arabidopsis ribosomal proteins." Plant Science 223 (June 2014): 134–45. http://dx.doi.org/10.1016/j.plantsci.2014.03.011.

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Washabaugh, Charles H., Martin P. Ontell, Jeffrey A. Kant, and Marcia Ontell. "Creatine kinase transcript accumulation: Effect of nerve during muscle development." Developmental Dynamics 215, no. 4 (1999): 285–96. http://dx.doi.org/10.1002/(sici)1097-0177(199908)215:4<285::aid-aja1>3.0.co;2-s.

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Surosky, R. T., and R. E. Esposito. "Early meiotic transcripts are highly unstable in Saccharomyces cerevisiae." Molecular and Cellular Biology 12, no. 9 (1992): 3948–58. http://dx.doi.org/10.1128/mcb.12.9.3948.

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Meiosis in Saccharomyces cerevisiae requires the induction of a large number of genes whose mRNAs accumulate at specific times during meiotic development. This study addresses the role of mRNA stability in the regulation of meiosis-specific gene expression. Evidence is provided below demonstrating that the levels of meiotic mRNAs are exquisitely regulated by both transcriptional control and RNA turnover. The data show that (i) early meiotic transcripts are extremely unstable when expressed during either vegetative growth or sporulation, and (ii) transcriptional induction, rather than RNA turnover, is the predominant mechanism responsible for meiosis-specific transcript accumulation. When genes encoding the early meiotic mRNAs are fused to other promoters and expressed during vegetative growth, their mRNA half-lives, of under 3 min, are among the shortest known in S. cerevisiae. Since these mRNAs are only twofold more stable when expressed during sporulation, we conclude that developmental regulation of mRNA turnover can be eliminated as a major contributor to meiosis-specific mRNA accumulation. The rapid degradation of the early mRNAs at all stages of the yeast life cycle, however, suggests that a specific RNA degradation system operates to maintain very low basal levels of these transcripts during vegetative growth and after their transient transcriptional induction in meiosis. Studies to identify specific cis-acting elements required for the rapid degradation of early meiotic transcripts support this idea. A series of deletion derivatives of one early meiosis-specific gene, SPO13, indicate that its mRNA contains determinants, located within the coding region, which contribute to the high instability of this transcript. Translation is another component of the degradation mechanism since frameshift and nonsense mutations within the SPO13 mRNA stabilize the transcript.

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Hassa, Paul, José Granado, Ernst Freydl, Urs Wäspi, and Robert Dudler. "Syringolin-Mediated Activation of the Pir7b Esterase Gene in Rice Cells Is Suppressed by Phosphatase Inhibitors." Molecular Plant-Microbe Interactions® 13, no. 3 (2000): 342–46. http://dx.doi.org/10.1094/mpmi.2000.13.3.342.

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Inoculation of rice plants (Oryza sativa) with the nonhost pathogen Pseudomonas syringae pv. syringae leads to the activation of defense-related genes and ultimately to induced resistance against the rice blast fungus Pyricularia oryzae. One of the molecular determinants of P. syringae pv. syringae that is recognized by the plant cells and evokes these defense responses is syringolin A, an elicitor that is secreted by the bacteria under appropriate conditions. In order to investigate signal transduction events elicited by syringolin A, the response of cultured rice cells to syringolin A application was analyzed. Cultured rice cells were able to sense syringolin A at concentrations in the nanomolar range as observed by the transient accumulation of Pir7b esterase transcripts. Syringolin A-mediated Pir7b transcript accumulation was inhibited by cycloheximide, indicating that de novo protein synthesis was required. Calyculin and okadaic acid, two protein phosphatase inhibitors, blocked Pir7b gene induction, whereas the serine/threonine protein kinase inhibitors staurosporine and K-252a had no effect on Pir7b transcript levels. Actin transcript levels were essentially not affected by inhibitor treatments over the experimental time span. These results imply that dephosphorylation of a phosphoprotein is an important step in the syringolin A-triggered signal transduction pathway.

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Flemetakis, Emmanouil, Rodica C. Efrose, Guilhem Desbrosses, et al. "Induction and Spatial Organization of Polyamine Biosynthesis During Nodule Development in Lotus japonicus." Molecular Plant-Microbe Interactions® 17, no. 12 (2004): 1283–93. http://dx.doi.org/10.1094/mpmi.2004.17.12.1283.

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Putrescine and other polyamines are produced by two alternative pathways in plants. One pathway starts with the enzyme arginine decarboxylase (ADC; EC 4.1.1.19), the other with ornithine decarboxylase (ODC; EC 4.1.1.17). Metabolite profiling of nitrogen-fixing Lotus japonicus nodules, using gas chromatography coupled to mass spectrometry, revealed a two- to sixfold increase in putrescine levels in mature nodules compared with other organs. Genes involved in polyamine biosynthesis in L. japonicus nodules were identified by isolating cDNA clones encoding ADC (LjADC1) and ODC (LjODC) from a nodule library. Searches of the public expressed sequence tag databases revealed the presence of a second gene encoding ADC (LjADC2). Real-time reverse-transcription-polymerase chain reaction analysis showed that LjADC1 and LjADC2 were expressed throughout the plant, while LjODC transcripts were detected only in nodules and roots. Induction of LjODC and LjADC gene expression during nodule development preceded symbiotic nitrogen fixation. Transcripts accumulation was maximal at 10 days postinfection, when a 6.5-fold increase in the transcript levels of LjODC was observed in comparison with the uninfected roots, while a twofold increase in the transcript levels of LjADC1 and LjADC2 was detected. At later stages of nodule development, transcripts for ADC drastically declined, while in the case of ODC, transcript accumulation was higher than that in roots until after 21 days postinfection. The expression profile of genes involved in putrescine biosynthesis correlated well with the expression patterns of genes involved in cell division and expansion, including a L. japonicus Cyclin D3 and an α-expansin gene. Spatial localization of LjODC and LjADC1 gene transcripts in developing nodules revealed that both transcripts were expressed in nodule inner cortical cells and in the central tissue. High levels of LjADC1 transcripts were also observed in both nodule and connecting root vascular tissue, suggesting that putrescine and other polyamines may be subject to long-distance transport. Our results indicate that polyamines are primarily involved in physiological and cellular processes involved in nodule development, rather than in processes that support directly symbiotic nitrogen fixation and assimilation.

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Caddick, Samuel E. K., Christopher J. Harrison, Ioanna Stavridou, Sue Johnson та Charles A. Brearley. "A lysine accumulation phenotype of ScIpk2Δ mutant yeast is rescued by Solanum tuberosum inositol phosphate multikinase". Biochemical Journal 403, № 3 (2007): 381–89. http://dx.doi.org/10.1042/bj20061772.

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Inositol phosphates and the enzymes that interconvert them are key regulators of diverse cellular processes including the transcriptional machinery of arginine synthesis [York (2006) Biochim. Biophys. Acta 1761, 552–559]. Despite considerable interest and debate surrounding the role of Saccharomyces cerevisiae inositol polyphosphate kinase (ScIPK2, ARG82, ARGRIII) and its inositol polyphosphate products in these processes, there is an absence of data describing how the transcripts of the arginine synthetic pathway, and the amino acid content of ScIpk2Δ, are altered under different nutrient regimes. We have cloned an IPMK (inositol phosphate multikinase) from Solanum tuberosum, StIPMK (GenBank® accession number EF362785), that despite considerable sequence divergence from ScIPK2, restores the arginine biosynthesis pathway transcripts ARG8, acetylornithine aminotransferase, and ARG3, ornithine carbamoyltransferase of ScIpk2Δ yeast to wild-type profiles. StIPMK also restores the amino acid profiles of mutant yeast to wild-type, and does so with ornithine or arginine as the sole nitrogen sources. Our data reveal a lysine accumulation phenotype in ScIpk2Δ yeast that is restored to a wild-type profile by expression of StIPMK, including restoration of the transcript profiles of lysine biosynthetic genes. The StIPMK protein shows only 18.6% identity with ScIPK2p which probably indicates that the rescue of transcript and diverse amino acid phenotypes is not mediated through a direct interaction of StIPMK with the ArgR–Mcm1 transcription factor complex that is a molecular partner of ScIPK2p.

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