Preferential deadenylation of Hsp70 mRNA plays a key role in regulating Hsp70 expression in Drosophila melanogaster

Heat Shock Responsive Gene Expression Modulated by mRNA Poly(A) Tail Length

Poly(A) tail length (PAL) has been implicated in the regulation of mRNA translation activities. However, the extent of such regulation at the transcriptome level is less understood in plants. Herein, we report the development and optimization of a large-scale sequencing technique called the Assay for PAL-sequencing (APAL-seq). To explore the role of PAL on post-transcriptional modification and translation, we performed PAL profiling of Arabidopsis transcriptome in response to heat shock. Transcripts of 2,477 genes were found to have variable PAL upon heat treatments. Further study of the transcripts of 14 potential heat-responsive genes identified two distinct groups of genes. In one group, PAL was heat stress-independent, and in the other, PAL was heat stress-sensitive. Meanwhile, the protein expression of HSP70 and HSP17.6C was determined to test the impact of PAL on translational activity. In the absence of heat stress, neither gene demonstrated protein expression; however, under gradual or abrupt heat stress, both transcripts showed enhanced protein expression with elongated PAL. Interestingly, HSP17.6C protein levels were positively correlated with the severity of heat treatment and peaked when treated with abrupt heat. Our results suggest that plant genes have a high variability of PALs and that PAL contributes to swift posttranslational stress responses.

The Dynamics of Cytoplasmic mRNA Metabolism

For all but a few mRNAs, the dynamics of metabolism are unknown. Here, we developed an experimental and analytical framework for examining these dynamics for mRNAs from thousands of genes. mRNAs of mouse fibroblasts exit the nucleus with diverse intragenic and intergenic poly(A)-tail lengths. Once in the cytoplasm, they have a broad (1000-fold) range of deadenylation rate constants, which correspond to cytoplasmic lifetimes. Indeed, with few exceptions, degradation appears to occur primarily through deadenylation-linked mechanisms, with little contribution from either endonucleolytic cleavage or deadenylation-independent decapping. Most mRNA molecules degrade only after their tail lengths fall below 25 nt. Decay rate constants of short-tailed mRNAs vary broadly (1000-fold) and are larger for short-tailed mRNAs that have previously undergone more rapid deadenylation. This coupling helps clear rapidly deadenylated mRNAs, enabling the large range in deadenylation rate constants to impart a similarly large range in stabilities.

DNA damage and translational response during detoxification from copper exposure in a wild population of Chironomus riparius

Copper is one of the predominant components of pesticides employed in agriculture and known to be highly toxic once it reaches aquatic organisms. The impact of sublethal concentrations of this metal on wild insects is not yet completely understood. Studies addressing alterations in different levels of gene expression are still lacking. We previously demonstrated that in a wild population of Chironomus riparius, HSP and CYP families of genes were up-regulated at the transcriptional level after copper exposure. Here, we analyse the impact of copper at the genomic, translational and protein functional level, obtaining a comprehensive picture of the molecular reply to this metal. We studied genotoxicity in C. riparius larvae by Comet Assay, the translational response by polysomal profiling and the detoxification capacity by the CYP450 enzymes activity. Fourth-instar larvae from a mountain stream polluted by agricultural land run-off (NE-Italy) were exposed for 3 h copper concentrations ≤ LC₅₀. We report DNA damage induced by copper, even at sublethal levels, as demonstrated by significant increases in all the comet parameters at concentrations ≥1 mg L^-1. By estimating the transcript-specific translational efficiency, we observe a specific up-regulation of CYP4G. Furthermore, the enzymatic activity of CYP450 enzymes is increased at all sublethal copper concentrations, confirming the role of this protein family in the detoxification processes. Surprisingly, the HSP transcripts are up-regulated at the transcriptional level, but these changes are buffered at the translational level suggesting the existence of still unknown post-transcriptional controls that may be connected to survival processes.

lncRNAs in Stress Response

All living organisms sense and respond to harmful changes in their intracellular and extracellular environment through complex signaling pathways that lead to changes in gene expression and cellular function in order to maintain homeostasis. Long non-coding RNAs (lncRNAs), a large and heterogeneous group of functional RNAs, play important roles in cellular response to stressful conditions. lncRNAs constitute a significant fraction of the genes differentially expressed in response to diverse stressful stimuli and, once induced, contribute to the regulation of downstream cellular processes, including feedback regulation of key stress response proteins. While many lncRNAs seem to be induced in response to a specific stress, there is significant overlap between lncRNAs induced in response to different stressful stimuli. In addition to stress-induced RNAs, several constitutively expressed lncRNAs also exert a strong regulatory impact on the stress response. Although our understanding of the contribution of lncRNAs to the cellular stress response is still highly rudimentary, the existing data point to the presence of a complex network of lncRNAs, miRNAs, and proteins in regulation of the cellular response to stress.

Non-coding RNAs turn up the heat: an emerging layer of novel regulators in the mammalian heat shock response

The field of non-coding RNA (ncRNA) has expanded over the last decade following the discoveries of several new classes of regulatory ncRNA. A growing amount of evidence now indicates that ncRNAs are involved even in the most fundamental of cellular processes. The heat shock response is no exception as ncRNAs are being identified as integral components of this process. Although this area of research is only in its infancy, this article focuses on several classes of regulatory ncRNA (i.e., miRNA, lncRNA, and circRNA), while summarizing their activities in mammalian heat shock. We also present an updated model integrating the traditional heat shock response with the activities of regulatory ncRNA. Our model expands on the mechanisms for efficient execution of the stress response, while offering a more comprehensive summary of the major regulators and responders in heat shock signaling. It is our hope that much of what is discussed herein may help researchers in integrating the fields of heat shock and ncRNA in mammals.

Robust heat-inducible gene expression by two endogenous hsp70-derived promoters in transgenic Aedes aegypti

Aedes aegypti is an important vector of the viruses that cause dengue fever, dengue haemorrhagic fever and yellow fever. Reverse genetic approaches to the study of gene function in this mosquito have been limited by the lack of a robust inducible promoter to allow precise temporal control over a protein-encoding or hairpin RNA transgene. Likewise, investigations into the molecular and biochemical basis of vector competence would benefit from the ability to activate an antipathogen molecule at specific times during infection. We have characterized the ability of genomic sequences derived from two Ae. aegypti heat shock protein 70 (hsp70) genes to drive heat-inducible expression of a reporter in both transient and germline transformation contexts. AaHsp70-luciferase transcripts accumulated specifically after heat shock, and displayed a pattern of rapid induction and decay similar to endogenous AaHsp70 genes. Luciferase expression in transgenic Ae. aegypti increased by ~25-50-fold in whole adults by 4 h after heat-shock, with significant activity (~20-fold) remaining at 24 h. Heat-induced expression was even more dramatic in midgut tissues, with one strain showing a ~2500-fold increase in luciferase activity. The AaHsp70 promoters described could be valuable for gene function studies as well as for the precise timing of the expression of antipathogen molecules.

Regulation of survival gene hsp70

Rapid expression of the survival gene, inducible heat shock protein 70 (hsp70), is critical for mounting cytoprotection against severe cellular stress, like elevated temperature. Hsp70 protein chaperones the refolding of heat-denatured peptides to minimize proteolytic degradation as a part of an eukaryotically conserved phenomenon referred to as the heat shock response. The physiologic stress associated with exercise, which can include elevated temperature, mechanical damage, hypoxia, lowered pH, and reactive oxygen species generation, may promote protein unfolding, leading to hsp70 gene expression in skeletal myofibers. Although the pre-transcriptional activation of hsp70 gene expression has been thoroughly reviewed, discussion of downstream hsp70 gene regulation is less extensive. The purpose of this brief review was to examine all levels of hsp70 gene regulation in response to heat stress and exercise with a special focus on skeletal myofibers where data are available. In general, while heat stress represses bulk gene expression, hsp70 mRNA expression is enhanced. Post-transcriptionally, intronless hsp70 mRNA circumvents a host of decay pathways, as well as heat stress-repressed pre-mRNA splicing and nuclear export. Pre-translationally, hsp70 mRNA is excluded from stress granules and preferentially translated during heat stress-repressed global cap-dependent translation. Post-translationally, nascent Hsp70 protein is thermodynamically stable at elevated temperatures, allowing for the commencement of chaperoning activity early after synthesis to attenuate the heat shock response and protect against subsequent injury. This review demonstrates that hsp70 mRNA expression is closely coupled with functional protein translation.

MicroRNAs in cardiac disease

MicroRNAs (miRs) are transcriptionally regulated single-strand RNAs that depress protein expression through posttranscriptional mRNA silencing. A host of recent studies have established essential roles for miRs in cardiac development and cardiac health. Regulated myocardial miR expression is observed in a variety of cardiac syndromes, and serum miR levels are being evaluated as disease biomarkers. The manipulation of miR levels in mouse hearts using genetic techniques or engineered miR mimetics and antagonists is elucidating the roles of specific cardiac miRs in cardiac development, and in the cardiac response to injury or stress, and heart disease. The ability to target multiple factors within a single biological response pathway by a given miR has prompted the development of small miR-targeting molecules that can be readily delivered and have sustained in vivo effects. These advances establish a foundation for novel diagnostics and new therapeutic approaches for myocardial infarction, cardiac hypertrophy, and heart failure.

Subunits of the Drosophila CCR4-NOT complex and their roles in mRNA deadenylation

The CCR4-NOT complex is the main enzyme catalyzing the deadenylation of mRNA. We have investigated the composition of this complex in Drosophila melanogaster by immunoprecipitation with a monoclonal antibody directed against NOT1. The CCR4, CAF1 (=POP2), NOT1, NOT2, NOT3, and CAF40 subunits were associated in a stable complex, but NOT4 was not. Factors known to be involved in mRNA regulation were prominent among the other proteins coprecipitated with the CCR4-NOT complex, as analyzed by mass spectrometry. The complex was localized mostly in the cytoplasm but did not appear to be a major component of P bodies. Of the known CCR4 paralogs, Nocturnin was found associated with the subunits of the CCR4-NOT complex, whereas Angel and 3635 were not. RNAi experiments in Schneider cells showed that CAF1, NOT1, NOT2, and NOT3 are required for bulk poly(A) shortening and hsp70 mRNA deadenylation, but knock-down of CCR4, CAF40, and NOT4 did not affect these processes. Overexpression of catalytically dead CAF1 had a dominant-negative effect on mRNA decay. In contrast, overexpression of inactive CCR4 had no effect. We conclude that CAF1 is the major catalytically important subunit of the CCR4-NOT complex in Drosophila Schneider cells. Nocturnin may also be involved in mRNA deadenylation, whereas there is no evidence for a similar role of Angel and 3635.

Degradation of hsp70 and other mRNAs in Drosophila via the 5' 3' pathway and its regulation by heat shock

Two general pathways of mRNA decay have been characterized in yeast. Both start with deadenylation. The major pathway then proceeds via cap hydrolysis and 5'-exonucleolytic degradation whereas the minor pathway consists of 3'-exonucleolytic decay followed by hydrolysis of the remaining cap structure. In higher eukaryotes, these pathways of mRNA decay are believed to be conserved but have not been well characterized. We have investigated the decay of the hsp70 mRNA in Drosophila Schneider cells. As shown by the use of reporter constructs, rapid deadenylation of this mRNA is directed by its 3'-untranslated region. The main deadenylase is the CCR4.NOT complex; the PAN nuclease makes a lesser contribution. Heat shock prevents deadenylation not only of the hsp70 but also of bulk mRNA. A completely deadenylated capped hsp70 mRNA decay intermediate accumulates transiently and is degraded via cap hydrolysis and 5'-decay. Thus, decapping is a slow step in the degradation pathway. Cap hydrolysis is also inhibited during heat shock. Degradation of reporter RNAs from the 3'-end became detectable only upon inhibition of 5'-decay and thus represents a minor decay pathway. Because two reporter RNAs and at least two endogenous mRNAs were degraded primarily from the 5'-end with cap hydrolysis as a slow step, this pathway appears to be of general importance for mRNA decay in Drosophila.

Translation-independent inhibition of mRNA deadenylation during stress in Saccharomyces cerevisiae

Post-transcriptional control mechanisms play an important role in regulating gene expression during cellular responses to stress. For example, many stresses inhibit translation, and at least some stresses inhibit mRNA turnover in yeast and mammalian cells. We show that hyperosmolarity, heat shock, and glucose deprivation stabilize multiple mRNAs in yeast, primarily through inhibition of deadenylation. Although these stresses inhibit translation and promote the movement of mRNAs into P-bodies, we also observed inhibition of deadenylation in cycloheximide-treated cells as well as in a mutant strain where translation initiation is impaired. This argues that inhibition of poly(A)-shortening is independent of the translational state of the mRNAs and can occur when mRNAs are localized in polysomes or are not engaged in translation. Analysis of pan2Delta or ccr4Delta strains indicates that stress inhibits the function of both the Ccr4p/Pop2p/Notp and the Pan2p/Pan3p deadenylases. We suggest that under stress, simultaneous repression of translation and deadenylation allows cells to selectively translate mRNAs specific to the stress response, while retaining the majority of the cytoplasmic pool of mRNAs for later reuse and recovery from stress. Moreover, because various cellular stresses also inhibit deadenylation in mammalian cells, this mechanism is likely to be a conserved aspect of the stress response.

Evaluation of the activities of the medfly and Drosophila hsp70 promoters in vivo in germ-line transformed medflies

The promoter of the hsp70 gene of Drosophila melanogaster has been widely used for the expression of foreign genes in other insects. It has been generally assumed that because this gene is highly conserved, its promoter will function efficiently in other species. We report the results of a quantitative comparison of the activities of the medfly and D. melanogaster hsp70 promoters in vivo in transformed medflies. We constructed transformed lines containing the lacZ reporter gene under the control of the two promoters by using Minos-mediated germ-line transformation. The activity of each promoter was evaluated in 15 transformed lines by beta-galactosidase quantitative assays. The heat-inducible activity of the medfly promoter was found several times higher than the respective activity of the heterologous D. melanogaster promoter. These results were confirmed by northern blot analysis and indicate that the D. melanogaster promoter does not work efficiently in medfly. The -263/+105 medfly promoter region that was used in this study was found able to drive heat shock expression of the lacZ reporter gene in all stages of medfly, except early embryonic stages, in a similar fashion to the endogenous hsp70 genes. However the heat inducible RNA levels driven from this promoter region were significantly lower than the endogenous hsp70 RNA levels, suggesting that additional upstream and/or downstream sequences to the -263/+105 region may be necessary for optimum function of the medfly hsp70 promoter in vivo.

Thermoprotection of synaptic transmission in aDrosophilaheat shock factor mutant is accompanied by increased expression of Hsp83 and DnaJ-1

In Drosophila larvae, acquired synaptic thermotolerance after heat shock has previously been shown to correlate with the induction of heat shock proteins (Hsps) including HSP70. We tested the hypothesis that synaptic thermotolerance would be significantly diminished in a temperature-sensitive strain ( Drosophila heat shock factor mutant hsf4), which has been reported not to be able to produce inducible Hsps in response to heat shock. Contrary to our hypothesis, considerable thermoprotection was still observed at hsf4larval synapses after heat shock. To investigate the cause of this thermoprotection, we conducted DNA microarray experiments to identify heat-induced transcript changes in these organisms. Transcripts of the hsp83, dnaJ-1 ( hsp40), and glutathione- S-transferase gstE1 genes were significantly upregulated in hsf4larvae after heat shock. In addition, increases in the levels of Hsp83 and DnaJ-1 proteins but not in the inducible form of Hsp70 were detected by Western blot analysis. The mode of heat shock administration differentially affected the relative transcript and translational changes for these chaperones. These results indicate that the compensatory upregulation of constitutively expressed Hsps, in the absence of the synthesis of the major inducible Hsp, Hsp70, could still provide substantial thermoprotection to both synapses and the whole organism.

Turning up the heat: The effects of thermal acclimation on the kinetics of hsp70 gene expression in the eurythermal goby, Gillichthys mirabilis

Most organisms respond to temperature fluctuations by altering the expression of an evolutionarily conserved family of proteins known as heat shock proteins (Hsps). Studies have shown Hsp expression and the activation of HSF1, one of the primary regulators of Hsp transcription, are highly malleable, varying with the recent thermal history of the organism; however, the mechanisms that confer plasticity to the regulation of this ubiquitous response are not well-understood. This study furthers our knowledge in this area by characterizing the activation kinetics of HSF1 and the corresponding transcription of hsp70 in the liver of the eurythermal goby, Gillichthys mirabilis, following a month-long acclimation at 13, 21 or 28 degrees C. Our data revealed HSF1 DNA-binding kinetics varied as a function of acclimation temperature and magnitude/duration of exposure, with gobies acclimated at 21 degrees C exhibiting the most robust response. Hsp70 mRNA followed a similar pattern with induction first occurring in the 13 and 21 degrees C fish, and then most robustly in the 28 degrees C group at 36 degrees C. The hsp70 mRNA induction pattern was corroborated by levels of HSF1 DNA-binding activity in each group and may have been lowest in the 28 degrees C group due to the 2-fold greater levels of hsp70 protein prior to thermal exposure. This study illustrates the integral role of HSF1 as a key regulator of Hsp induction and helps explain the plasticity of this response in ectothermic organisms.

Reduced stress tolerance of glutamine-deprived human monocytic cells is associated with selective down-regulation of Hsp70 by decreased mRNA stability

In critically ill patients, clinicians observe a reverse correlation of survival and a decreased plasma concentration of the most abundant free amino acid, glutamine (Gln). However, in this context, the role of Gln remains largely elusive. Gln is used as an energy substrate by monocytes. Gln deprivation of these cells results in an increased susceptibility to cell stress and apoptosis, as well as in a reduced responsiveness to pro-inflammatory stimuli. We performed a systematic study to elucidate the molecular mechanism by which Gln depletion affects the heat stress response of the monocytic cell line U937. Proteomic analysis revealed that Gln depletion was associated with specific changes in the protein expression pattern. However, the overall level of tRNA-bound Gln remained unaffected. The stress protein heat shock protein (Hsp) 70 showed the highest reduction in protein synthesis. This was due to enhanced mRNA decay during Gln starvation while the transcriptional and the translational control of Hsp70 expression remained unchanged. A physiological Gln concentration and above was found to be necessary for maximum Hsp70 accumulation upon heat shock. Thus, the study shows a specific link between Gln metabolism and the regulation of heat shock proteins.

Messenger RNA turnover in eukaryotes: pathways and enzymes

The control of mRNA degradation is an important component of the regulation of gene expression since the steady-state concentration of mRNA is determined both by the rates of synthesis and of decay. Two general pathways of mRNA decay have been described in eukaryotes. Both pathways share the exonucleolytic removal of the poly(A) tail (deadenylation) as the first step. In one pathway, deadenylation is followed by the hydrolysis of the cap and processive degradation of the mRNA body by a 5' exonuclease. In the second pathway, the mRNA body is degraded by a complex of 3' exonucleases before the remaining cap structure is hydrolyzed. This review discusses the proteins involved in the catalysis and control of both decay pathways.

Comparative expression analysis of two paralogous Hsp70s in rainbow trout cells exposed to heat stress

Heat-shock protein 70 (Hsp70) is the major stress-inducible protein in vertebrates and highly conserved throughout evolution. To accurately investigate the mRNA expression profiles of multiple Hsp70s in rainbow trout Oncorhynchus mykiss, we isolated full-length cDNA clones encoding Hsp70 from the fish and investigated their mRNA expression profiles during heat stress. Consequently, two Hsp70s, Hsp70a and Hsp70b, were identified and found to have 98.1% identity in their deduced amino acid sequences. Southern blot analysis indicated that the two Hsp70s are encoded by distinct genes in the genome. Northern blot analysis showed that each of Hsp70a and Hsp70b expressed two mRNA species having different sizes by heat stress in rainbow trout RTG-2 cells. The induction levels of total Hsp70b mRNAs were consistently higher than Hsp70a counterparts during heat stress, although the expression profiles of the two genes were similar to each other in temperature shift and time course experiments. Interestingly, an mRNA species with a larger molecular size was expressed only under severe heat stress not less than 28 degrees C irrespective of Hsp70a and Hsp70b. These results suggest that the comprehensive identification of duplicated genes is a prerequisite to examining the gene expression profiles for tetraploid species such as rainbow trout.

Magnitude and Duration of Thermal Stress Determine Kinetics ofhspGene Regulation in the GobyGillichthys mirabilis

The stress-induced transcription of heat shock genes is controlled by heat shock transcription factor 1 (HSF1), which becomes activated in response to heat and other protein denaturants. In previous research on the eurythermal goby Gillichthys mirabilis, thermal activation of HSF1 was shown to vary as a function of acclimation temperature, suggesting the mechanistic importance of HSF1 activation to the plasticity of heat shock protein (Hsp) induction temperature. We examined the effect of season on the thermal activation of HSF1 in G. mirabilis, as well as the relative kinetics of HSF1 activation and Hsp70 mRNA production at ecologically relevant temperatures. There was no predictable seasonality in the thermal activation of HSF1, perhaps due to the existence of stressors, in addition to heat, acting in the field. Concentrations of Hsp70, a negative regulator of HSF1, as well as those of HSF1, varied with collection date. The rapidity of HSF1 activation and of Hsp70 mRNA synthesis increased with laboratory exposure temperature. Furthermore, Hsp70 mRNA production was more sustained at 35 degrees C than at 30 degrees C. Therefore, both the magnitude and the duration of a heat shock are important in determining the intensity of heat shock gene induction.

A complex containing the CCR4 and CAF1 proteins is involved in mRNA deadenylation in Drosophila

The CCR4-NOT complex is the major enzyme catalyzing mRNA deadenylation in Saccharomyces cerevisiae. We have identified homologs for almost all subunits of this complex in the Drosophila genome. Biochemical fractionation showed that the two likely catalytic subunits, CCR4 and CAF1, were associated with each other and with a poly(A)-specific 3' exonuclease activity. In Drosophila, the CCR4 and CAF1 proteins were ubiquitously expressed and present in cytoplasmic foci. Individual knock-down of several potential subunits of the Drosophila CCR4-NOT complex by RNAi in tissue culture cells led to a lengthening of bulk mRNA poly(A) tails. Knock-down of two individual subunits also interfered with the rapid deadenylation of Hsp70 mRNA during recovery from heat shock. Similarly, ccr4 mutant flies had elongated bulk poly(A) and a defect in Hsp70 mRNA deadenylation. A minor increase in bulk poly(A) tail length was also observed in Rga mutant flies, which are affected in the NOT2 subunit. The data show that the CCR4-NOT complex is conserved in Drosophila melanogaster and plays a role in general and regulated mRNA deadenylation.

Regulation of heat shock proteins, Hsp70 and Hsp64, in heat-shocked Malpighian tubules of Drosophila melanogaster larvae

It is known from earlier studies that the heat shock (HS) response in Malpighian tubules (MTs) of Drosophila larvae is different from that in other tissues because instead of the Hsp70 and other common heat shock proteins, Hsp64 and certain other new proteins are induced immediately after HS. In the present study, we examined the kinetics of the synthesis of Hsp70 and Hsp64 immediately after HS and during recovery from HS by 35S-methionine labeling and Western blotting. In addition, we also examined the transcriptional activity of hsp70 genes in larval MT cells at different times after HS by in situ hybridization and Northern blotting. The HS-induced synthesis of Hsp64 ceased by 1 hour of recovery from the HS when synthesis of the Hsp70 commenced. Our results revealed that the induced synthesis of Hsp64 immediately after HS was dependent on new transcription. Although the levels of Hsp70 in MT cells rapidly increased after its synthesis began during recovery, the levels of Hsp64 remained unaltered irrespective of its new synthesis occurring during or after HS. Inhibition of new Hsp64 synthesis by transcriptional or translational inhibitors also did not affect the total amount of this protein in MTs. The Hsp64 polypeptides synthesized in response to HS are degraded rapidly. Apparently, the cells in MTs maintain a balance between new synthesis of Hsp64 and its turnover so that under all conditions a more or less constant level of this protein is maintained. Although the Hsp70 synthesis started only after 1 hour of recovery, the hsp70 genes were transcriptionally activated immediately after HS and they continued to transcribe till at least 4 hours after the HS. The hsp70 transcripts in MT cells that recovered for 2 hours or longer did not contain the 3' untranslated regions (UTRs), which may allow their longer stability and translatability at normal temperature. Synthesis of Hsp70 during recovery period was dependent on continuing transcription. Assessment of the beta-galactosidase activity in 2 transgenic lines carrying the LacZ reporter gene under hsp70 promoter and different lengths of the 5'UTR suggested that the delayed translation of hsp70 transcripts in MTs is probably regulated by some elements in the 5'UTR.

Ectopic expression ofDrosophilaELAV and human HuD inDrosophilawing disc cells reveals functional distinctions and similarities

Drosophila ELAV and human HuD are two neuronal RNA binding proteins that show remarkable sequence homology, yet differ in their respective documented roles in post-transcriptional regulation. ELAV regulates neural-specific alternative splicing of specific transcripts, and HuD stabilizes specific mRNAs that are otherwise unstable due to AU-rich elements(AREs) in their 3′ untranslated region (UTR). AREs are major determinants of transcript stability in mammalian cells. The role of each of these proteins was investigated and compared, by ectopically expressing them in Drosophila imaginal wing disc cells, which lack endogenous expression of either protein. The effect of the ectopic expression of ELAV and HuD was assessed on two sets of green fluorescent protein reporter transgenes,which were all driven with a broadly expressing promoter. Each set consisted of three reporter transgenes: (1) with an uninterrupted open reading frame(ORF); (2) with a constitutively spliced intron inserted into the ORF; and (3)with the intron nASI whose splicing is regulated in neurons by ELAV,inserted into the ORF. The two sets differed from each other only in their 3′UTR: Heat-shock-protein-70Ab (Hsp70Ab) trailer with ARE-like characteristics or Actin 5C (Act5C) trailer. Our results show that:(1) both ectopically expressed ELAV and HuD can enhance expression of transgenes with the Hsp70Ab 3′UTR, but not of transgenes with Act5C 3′UTR; (2) this enhancement is accompanied by an increase in mRNA level; (3) only ELAV can induce neural-specific splicing of nASI; and (4) although HuD is localized primarily to the cytoplasm,ELAV is localized to both the cytoplasm and the nucleus.

Tissue- and development-specific induction and turnover of hsp70 transcripts from loci 87A and 87C after heat shock and during recovery inDrosophila melanogaster

The haploid genome of Drosophila melanogaster normally carries at least five nearly identical copies of heat-shock-inducible hsp70 genes, two copies at the 87A7 and three copies at the 87C1 chromosome sites. We used in situ hybridization of the cDNA, which hybridizes with transcripts of all five hsp70 genes, and of two 3′ untranslated region (3′UTR; specific for the 87A7- and 87C1-type hsp70 transcripts) riboprobes to cellular RNA to examine whether all these copies were similarly induced by heat shock in different cell types of D. melanogaster. Our results revealed remarkable differences not only in the heat-shock-inducibility of the hsp70 genes at the 87A7 and 87C1 loci, but also in their post-transcriptional metabolism, such as the stability of the transcripts and of their 3′UTRs in different cell types in developing embryos and in larval and adult tissues. Our results also revealed the constitutive presence of the heat-shock-inducible form of Hsp70 in a subset of late spermatogonial cells from the second-instar larval stage onwards. We suggest that the multiple copies of the stress-inducible hsp70 genes do not exist in the genome of D. melanogaster only to produce large amounts of the Hsp70 rapidly and at short notice, but that they are specifically regulated in a developmental-stage-specific manner. It is likely that the cost/benefit ratio of not producing or of producing a defined amount of Hsp70 under stress conditions varies for different cell types and under different physiological conditions and, accordingly, specific regulatory mechanisms operating at the transcriptional and post-transcriptional levels have evolved.

Developmental regulation of heat shock protein 83 in Leishmania. 3' processing and mRNA stability control transcript abundance, and translation id directed by a determinant in the 3'-untranslated region

Developmental gene regulation in trypanosomatids proceeds exclusively by post-transcriptional mechanisms. Stability and abundance of heat shock protein (HSP)70 and HSP83 transcripts in Leishmania increase at mammalian-like temperatures, and their translation is enhanced. Here we report that the 3'-untranslated region (UTR) of HSP83 (886 nucleotides) confers the temperature-dependent pattern of regulation on a chloramphenicol acetyltransferase (CAT) reporter transcript. We also show that the majority of the 3'-UTR sequences are required for increasing mRNA stability during heat shock. Processing of the HSP70 and HSP83 primary transcripts to poly(A)(+) mRNA was more efficient during heat shock; therefore, even when stability at 33 degrees C was reduced by deletions in the 3'-UTR, transcripts still accumulated to comparable and even higher levels. Translation of heat shock transcripts in Leishmania increases dramatically upon temperature elevation. Unlike in other eukaryotes in which the 5'-UTR confers preferential translation on heat shock transcripts, we show that translational control of HSP83 in Leishmania originates from its 3'-UTR. The 5'-UTR alone cannot induce translation during heat shock, but it has a minor contribution when combined with the HSP83 3'-UTR. We identified an element located between positions 201 and 472 of the 3'-UTR which is essential for increasing translation of the CAT-HSP83 reporter RNA at 33-37 degrees C. This region confers preferential translation during heat shock even in transcripts that were less stable. Thus, investigating the traditionally conserved heat shock response reveals that Leishmania parasites use unique pathways for translational control.

Differential gene expression in drug metabolism and toxicology: practicalities, problems and potential

1. An important feature of the work of many molecular biologists is identifying which genes are switched on and off in a cell under different environmental conditions or subsequent to xenobiotic challenge. Such information has many uses, including the deciphering of molecular pathways and facilitating the development of new experimental and diagnostic procedures. However, the student of gene hunting should be forgiven for perhaps becoming confused by the mountain of information available as there appears to be almost as many methods of discovering differentially expressed genes as there are research groups using the technique. 2. The aim of this review was to clarify the main methods of differential gene expression analysis and the mechanistic principles underlying them. Also included is a discussion on some of the practical aspects of using this technique. Emphasis is placed on the so-called 'open' systems, which require no prior knowledge of the genes contained within the study model. Whilst these will eventually be replaced by 'closed' systems in the study of human, mouse and other commonly studied laboratory animals, they will remain a powerful tool for those examining less fashionable models. 3. The use of suppression-PCR subtractive hybridization is exemplified in the identification of up- and down-regulated genes in rat liver following exposure to phenobarbital, a well-known inducer of the drug metabolizing enzymes. 4. Differential gene display provides a coherent platform for building libraries and microchip arrays of 'gene fingerprints' characteristic of known enzyme inducers and xenobiotic toxicants, which may be interrogated subsequently for the identification and characterization of xenobiotics of unknown biological properties.

Messenger RNA-binding properties of nonpolysomal ribonucleoproteins from heat-stressed tomato cells

Most cells experiencing heat stress reprogram their translational machinery to favor the synthesis of heat-stress proteins. Translation of other transcripts is almost completely repressed, but most untranslated messengers are not degraded. In contrast to yeast, Drosophila melanogaster, and HeLa cells, plant cells store repressed messengers in cytoplasmic nonpolysomal ribonucleoproteins (RNPs). To follow the fate of untranslated transcripts, we studied protein composition, mRNA content, and RNA-binding properties of nonpolysomal RNPs from heat-stressed tomato (Lycopersicon peruvianum) cells. Contrary to the selective interaction in vivo, RNPs isolated from tomato cells bound both stress-induced and repressed messengers, suggesting that the selection mechanism resides elsewhere. This binding was independent of a cap or a poly(A) tail. The possible role of proteasomes and heat-stress granules (HSGs) in mRNA storage is a topic of debate. We found in vitro messenger-RNA-binding activity in messenger RNP fractions free of C2-subunit-containing proteasomes and HSGs. In addition, mRNAs introduced into tobacco (Nicotiana plumbaginifolia) protoplasts were found in the cytoplasm but were not associated with HSGs.

Developmentally regulated nuclear transport of transcription factors in Drosophila embryos enable the heat shock response

Hsp70 is a broadly conserved thermotolerance factor, but inhibits growth at normal temperatures and cannot be induced in early embryos. We report that in Drosophila embryos the temporal and spatial patterns of Hsp70 inducibility were unexpectedly complex, with striking differences between the soma and the germline. In both, regulation occurred at the level of transcription. During the refractory period for Hsp70 induction, HSF (heat-shock transcription factor) exhibited specific DNA-binding activity characteristic of activation in extracts of heated embryos. Remarkably, however, HSF was restricted to the cytoplasm in intact embryos even after heat shock. HSF moved from the cytoplasm to the nucleus in the absence of heat precisely when the capacity to induce Hsp70 was acquired (cycle 12 of the germline, cycle 13 in the soma). During oogenesis, Hsp70 inducibility was lost in nurse cells around stage 10, in a posterior-to-anterior gradient and HSF redistributed from nucleus to cytoplasm in the same spatiotemporal pattern. In a highly inbred derivative of the Samarkind strain, HSF moved into embryonic nuclei earlier than in our standard wild-type strain. Correspondingly, Hsp70 was inducible earlier, confirming that nuclear transport of HSF controls the inducibility of Hsp70 in early embryos. We also report for the first time the nuclear import patterns of two general transcription factors, RNA polymerase subunit Ilc and TATA binding protein (TBP). Both enter nuclei in a highly synchronous manner, independently of each other and of HSF. The import of TBP coincides with the first reported appearance of transcripts in the embryo. We suggest that the potentiation of general and heat shock-specific transcription in Drosophila embryos is controlled by the developmentally programmed relocalization of general and heat shock-specific transcription factors. Restricted nuclear entry of HSF represents a newly described mechanism for regulating the heat-shock response.

Marked differences between avian and mammalian testicular cells in the heat shock induction and polyadenylation of Hsp70 and ubiquitin transcripts

Mammalian male germ cells undergo apoptosis at the body's internal temperature of 37 degrees C. Birds, however, are unique among homeothermic animals in developing spermatogenesis at the elevated avian internal body temperature of 40-41 degrees C. To shed light on the mechanisms that maintain an efficient avian spermatogenesis at elevated temperatures we compared, in mouse and chicken testicular cells, the expression of genes that are essential for stress resistance: Hsp70 and ubiquitin. While the expression of Hsp70 and ubiquitin did not change upon heat shock in mouse testicular cells, both the amount and polyadenylation of Hsp70 and ubiquitin transcripts increased when male germ cells from adult chicken testis were exposed to elevated temperatures.

Temperature adaptation of house keeping and heat shock gene expression in Neurospora crassa

Adaptation of house keeping and heat shock gene expression was determined in Neurospora crassa during continuous exposure to different temperatures. Steady-state values of total protein synthesis differed little after incubation for 24 h at temperatures between 15 and 42 degreesC. Adaptation kinetics at 42 degreesC showed an initial, transient inhibition of total protein synthesis. Similar kinetics were observed with actin synthesis and tubulin mRNA. A priming 1-h heat shock of 42 degreesC 2 h prior to a second continuous exposure to 42 degreesC abolished the inhibitory effect of the second treatment and resulted in "acquired translational tolerance." Steady-state values of HSP70 synthesis rates revealed increasing levels with increasing temperatures after incubation for 24 h at different temperatures. Adaptation kinetics of the synthesis rates of different HSPs in vivo revealed maximal rates after 2 h and then a decrease to the elevated steady-state levels. The total amount of the major constitutive and inducible HSP70 isoform as determined by Western blots reached a maximum 2 h after the beginning of 42 degreesC exposure and only a slight decrease (25%) of the maximal value after 24 h. The inducible isoform of HSP70, in contrast, reached a maximum after 4-8 h and then decreased strongly after 24 h. HSP mRNAs reached maximal amounts 45-60 min after the beginning of 42 degreesC exposure and then declined after 8 h as determined by in vitro translation. Northern blots revealed maximal mRNA amounts of the inducible HSP70 after 30 min and zero amounts after 4 h exposure to 42 degreesC. After a shift to 42 degreesC HSP70 isoforms were immediately translocated into the nucleus and reshuttled into the cytoplasm during the following 6 h. The nuclear content of HSP70 remained elevated during the adapted steady state at 24 h. It is concluded that the adapted state after 24 h is based on enhanced amounts of constitutive isoforms in the cytoplasm and in the nucleus, whereas the inducible isoforms of HSP70 show faster adaptation kinetics.

Accumulation of Hsp70 mRNA under environmental stresses in diapausing and nondiapausing adults of Drosophila triauraria

Drosophila triauraria entered reproductive diapause in response to short daylengths and acquired tolerance to heat, cold and desiccation. In this species, the heat-shock response (accumulation of Hsp70 mRNA in response to heat) occurred at 27-41 degrees C, and the level of Hsp70 mRNA did not differ between diapausing and nondiapausing individuals. Hsp70 mRNA was also induced by exposure to -4 or -8 degrees C. However, it was scarcely detected just after the exposure to cold, but accumulated when flies were maintained at normal temperature following the exposure to cold. The level of Hsp70 mRNA was lower in diapausing individuals than in nondiapausing ones when exposed to -4 degrees C, but was not different between them when exposed to -8 degrees C. This species did not synthesize Hsp70 mRNA under desiccation stress irrespective of the diapause state. These results suggest that diapausing individuals of this species acquired tolerance to heat, cold and desiccation independent of the transcriptional regulation of the hsp70 gene

Stress (heat shock) proteins: molecular chaperones in cardiovascular biology and disease

How a cell responds to stress is a central problem in cardiovascular biology. Diverse physiological stresses (eg, heat, hemodynamics, mutant proteins, and oxidative injury) produce multiple changes in a cell that ultimately affect protein structures and function. Cells from different phyla initiate a cascade of events that engage essential proteins, the molecular chaperones, in decisions to repair or degrade damaged proteins as a defense strategy to ensure survival. Accumulative evidence indicates that molecular chaperones such as the heat shock family of stress proteins (HSPs) actively participate in an array of cellular processes, including cytoprotection. The versatility of the ubiquitous HSP family is further enhanced by stress-inducible regulatory networks, both at the transcriptional and posttranscriptional levels. In the present review, we discuss the regulation and function of HSP chaperones and their clinical significance in conditions such as cardiac hypertrophy, vascular wall injury, cardiac surgery, ischemic preconditioning, aging, and, conceivably, mutations in genes encoding contractile proteins and ion channels.

Differential display-mediated isolation of a genomic sequence for a putative mitochondrial LMW HSP specifically expressed in condition of induced thermotolerance in Arabidopsis thaliana (L.) heynh

Plants of Arabidopsis thaliana pre-treated at 37 degrees C for 2 h can survive an otherwise lethal heat shock at 45 degrees C. Differential display reverse transcriptase-PCR (DDRT-PCR) was utilized to clone DNA fragments corresponding to mRNAs specifically expressed in conditions of induced thermotolerance or of expression of thermotolerance. One of these DDRT-PCR fragments enabled the isolation of a genomic clone pAt1.3EX, containing the sequence Athsp23.5, the gene for a low-molecular-weight (LMW) heat shock protein (HSP), AtHSP23.5. Athsp23.5 is low- or single-copy in the Arabidopsis genome and its open reading frame is interrupted by a 137 bp intron. Analysis of the sequence suggests AtHSP23.5 is targeted to the mitochondrion. The steady-state level of the AtHSP23.5 mRNA varied significantly according to the heat treatment, increasing on heat shock (transfer from 22 degrees C to 37 degrees C), with a further increase during expression of thermotolerance (transfer from 22 degrees C to 37 degrees C and then to 45 degrees C). Expression was low after an abrupt stress (from 22 degrees C to 45 degrees C). This behaviour was different from that observed for other LMW HSP mRNAs that were present at high level at 37 degrees C, but did not increase significantly in condition of expression of thermotolerance, and reached a considerable steady-state level also during the abrupt stress at 45 degrees C. The retrotranscription of AtHSP23.5 mRNA followed by amplification with two primers encompassing the intron allowed for the isolation of an almost full-length cDNA sequence. The sequence analysis of the two cDNAs obtained from condition 22 degrees C-->37 degrees C and condition 22 degrees C-->45 degrees C suggested that in both cases the intron had been correctly spliced. The importance of correct intron splicing in survival at high temperatures and the role of mitochondrial HSP in induction and expression of thermotolerance are discussed.

Cordycepin blocks recovery of non-heat-shock mRNA translation following heat shock in Drosophila

Treatment of cells with cordycepin (3-deoxyadenosine), an inhibitor of cytoplasmic adenylation, blocks the restoration of normal translation following heat shock. Cordycepin also reduces heat-shock protein 70 (Hsp70) protein synthesis greater than 10-fold, while having little to no effect on mRNA accumulation. Parallel analysis of the poly(A)-binding protein detects no change in its abundance during heat shock or subsequent recovery. These results suggest that normal, non-heat-shock mRNA translational repression during heat shock may be caused by deadenylation, and that readenylation is required for restoration of activity. However, three independent analyses of the adenylation status of mRNAs during heat shock and recovery indicate that no significant changes in polyadenylation occur. (a) The total poly(A) content decreases by only about 10% during heat shock; (b) the size of the poly(A) tract decreases only marginally, from an average length of 75-90 nucleotides in non-heated cells to 45-60 nucleotides during heat shock; (c) virtually all mRNAs bind to oligo d(T)-cellulose, whether extracted from normal-temperature, heat-shock or recovered cells. Our results are most consistent with a model where the process of readenylation, rather than the specific poly(A) tail length, influences translational activation during recovery, paralleling a proposed model for the activation of translation during Xenopus oocyte maturation.

mRNA stability in mammalian cells

This review concerns how cytoplasmic mRNA half-lives are regulated and how mRNA decay rates influence gene expression. mRNA stability influences gene expression in virtually all organisms, from bacteria to mammals, and the abundance of a particular mRNA can fluctuate manyfold following a change in the mRNA half-life, without any change in transcription. The processes that regulate mRNA half-lives can, in turn, affect how cells grow, differentiate, and respond to their environment. Three major questions are addressed. Which sequences in mRNAs determine their half-lives? Which enzymes degrade mRNAs? Which (trans-acting) factors regulate mRNA stability, and how do they function? The following specific topics are discussed: techniques for measuring eukaryotic mRNA stability and for calculating decay constants, mRNA decay pathways, mRNases, proteins that bind to sequences shared among many mRNAs [like poly(A)- and AU-rich-binding proteins] and proteins that bind to specific mRNAs (like the c-myc coding-region determinant-binding protein), how environmental factors like hormones and growth factors affect mRNA stability, and how translation and mRNA stability are linked. Some perspectives and predictions for future research directions are summarized at the end.

mRNA stability in mammalian cells

This review concerns how cytoplasmic mRNA half-lives are regulated and how mRNA decay rates influence gene expression. mRNA stability influences gene expression in virtually all organisms, from bacteria to mammals, and the abundance of a particular mRNA can fluctuate manyfold following a change in the mRNA half-life, without any change in transcription. The processes that regulate mRNA half-lives can, in turn, affect how cells grow, differentiate, and respond to their environment. Three major questions are addressed. Which sequences in mRNAs determine their half-lives? Which enzymes degrade mRNAs? Which (trans-acting) factors regulate mRNA stability, and how do they function? The following specific topics are discussed: techniques for measuring eukaryotic mRNA stability and for calculating decay constants, mRNA decay pathways, mRNases, proteins that bind to sequences shared among many mRNAs [like poly(A)- and AU-rich-binding proteins] and proteins that bind to specific mRNAs (like the c-myc coding-region determinant-binding protein), how environmental factors like hormones and growth factors affect mRNA stability, and how translation and mRNA stability are linked. Some perspectives and predictions for future research directions are summarized at the end.