Hydrogen peroxide induces the expression of adapt15, a novel RNA associated with polysomes in hamster HA-1 cells

Defining lncRNAs Correlated with CHO Cell Growth and IgG Productivity by RNA-Seq

How the long non-coding RNA (lncRNA) genome in recombinant protein producing Chinese hamster ovary (CHO) cell lines relates to phenotype is not well described. We therefore defined the CHO cell lncRNA transcriptome from cells grown in controlled miniature bioreactors under fed-batch conditions using RNA-Seq to identify lncRNAs and how the expression of these changes throughout growth and between IgG producers. We identify lncRNAs including Adapt15, linked to ER stress, GAS5, linked to mTOR signaling/growth arrest, and PVT1, linked to Myc expression, which are differentially regulated during fed-batch culture and whose expression correlates to productivity and growth. Changes in (non)-coding RNA expression between the seed train and the equivalent day of fed-batch culture are also reported and compared with existing datasets. Collectively, we present a comprehensive lncRNA CHO cell profiling and identify targets for engineering growth and productivity characteristics of CHO cells.

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The CHO cell lncRNA transcriptome is defined using RNA-Seq

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Correlations between lncRNA expression and CHO cell growth and IgG productivity found

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Expression of lncRNAs involved in ER stress correlates to productivity

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Expression of lncRNAs involved in mTOR signaling/growth arrest correlates to growth

Long Noncoding RNAs in the Regulation of Oxidative Stress

Oxidative stress takes responsibility for various diseases, such as chronic obstructive pulmonary disease (COPD), Alzheimer's disease (AD), and cardiovascular disease; nevertheless, there is still a lack of specific biomarkers for the guidance of diagnosis and treatment of oxidative stress-related diseases. In recent years, growing studies have documented that oxidative stress has crucial correlations with long noncoding RNAs (lncRNAs), which have been identified as important transcriptions involving the process of oxidative stress, inflammation, etc. and been regarded as the potential specific biomarkers. In this paper, we review links between oxidative stress and lncRNAs, highlight lncRNAs that refer to oxidative stress, and conclude that lncRNAs have played a negative or positive role in the oxidation/antioxidant system, which may be helpful for the further investigation of specific biomarkers of oxidative stress-related diseases.

Global insights into the Chinese hamster and CHO cell transcriptomes

Transcriptomics is increasingly being used on Chinese hamster ovary (CHO) cells to unveil physiological insights related to their performance during production processes. The rich transcriptome data can be exploited to provide impetus for systems investigation such as modeling the central carbon metabolism or glycosylation pathways, or even building genome-scale models. To harness the power of transcriptome assays, we assembled and annotated a set of RNA-Seq data from multiple CHO cell lines and Chinese hamster tissues, and constructed a DNA microarray. The identity of genes involved in major functional pathways and their transcript levels generated in this study will serve as a reference for future studies employing kinetic models. In particular, the data on glycolysis and glycosylation pathways indicate that the variability of gene expression level among different cell lines and tissues may contribute to their differences in metabolism and glycosylation patterns. Thereby, these insights can potentially lead to opportunities for cell engineering. This repertoire of transcriptome data also enables the identification of potential sequence variants in cell lines and allows tracing of cell lineages. Overall the study is an illustration of the potential benefit of RNA-Seq that is yet to be exploited.

On the classification of long non-coding RNAs

Long non-coding RNAs (lncRNAs) have been found to perform various functions in a wide variety of important biological processes. To make easier interpretation of lncRNA functionality and conduct deep mining on these transcribed sequences, it is convenient to classify lncRNAs into different groups. Here, we summarize classification methods of lncRNAs according to their four major features, namely, genomic location and context, effect exerted on DNA sequences, mechanism of functioning and their targeting mechanism. In combination with the presently available function annotations, we explore potential relationships between different classification categories, and generalize and compare biological features of different lncRNAs within each category. Finally, we present our view on potential further studies. We believe that the classifications of lncRNAs as indicated above are of fundamental importance for lncRNA studies, helpful for further investigation of specific lncRNAs, for formulation of new hypothesis based on different features of lncRNA and for exploration of the underlying lncRNA functional mechanisms.

A conserved role for the 20S proteasome and Nrf2 transcription factor in oxidative stress adaptation in mammals, Caenorhabditis elegans and Drosophila melanogaster

In mammalian cells, hydrogen peroxide (H(2)O(2))-induced adaptation to oxidative stress is strongly dependent on an Nrf2 transcription factor-mediated increase in the 20S proteasome. Here, we report that both Caenorhabditis elegans nematode worms and Drosophila melanogaster fruit flies are also capable of adapting to oxidative stress with H(2)O(2) pre-treatment. As in mammalian cells, this adaptive response in worms and flies involves an increase in proteolytic activity and increased expression of the 20S proteasome, but not of the 26S proteasome. We also found that the increase in 20S proteasome expression in both worms and flies, as in mammalian cells, is important for the adaptive response, and that it is mediated by the SKN-1 and CNC-C orthologs of the mammalian Nrf2 transcription factor, respectively. These studies demonstrate that stress mechanisms operative in cell culture also apply in disparate intact organisms across a wide biological diversity.

Long non-coding RNAs coordinate cellular responses to stress

Following the initial discovery of the heat shock RNA omega (hsrω) gene of Drosophila melanogaster to be non-coding (nc) and also inducible by cell stress, other stress-inducible long non-coding RNAs (lncRNA) have been described in diverse organisms. In view of the rapid sequence divergence of lncRNAs, present knowledge of stress trasncriptome is limited and fragmented. Several known stress-related lncRNAs, associated with specific nuclear speckled domains or nucleolus, provide structural base for sequestering diverse RNA-processing/regulatory proteins. Others have roles in transcriptional or translational inhibition during stress or in signaling pathways; functions of several other lncRNAs are not yet known. Most stress-related lncRNAs act primarily by modulating activity of the proteins to which they bind or by sequestering specific sets of proteins away from the active pool. A common emerging theme is that a given lncRNA targets one or more protein/s with key role/s in the cascade of events triggered by the stress and therefore has a widespread integrative effect. Since proteins associate with RNA through short sequence motifs, the overall base sequence of functionally similar ncRNAs is often not conserved except for specific motifs. The rapid evolvability of ncRNA sequences provides elegant modules for adaptability to changing environment as binding of one or the other protein to ncRNA can alter its structure and functions in distinct ways. Thus the stress-related lncRNAs act as hubs in the cellular networks to coordinate activities of the members within and between different networks to maintain cellular homeostasis for survival or to trigger cell death.

Long noncoding RNAs in cell biology

Whole genome transcriptomic analyses have identified large numbers of dynamically expressed long non-protein-coding RNAs (lncRNAs) in mammals and other animals whose functions are, as yet, largely unknown. Here we summarize the growing evidence that lncRNAs, like mRNAs, can be trafficked to and function in a wide variety of subcellular locations. Investigation of the subcellular distribution of lncRNAs has the potential to greatly expand our knowledge not only of the function of lncRNAs but also of cell biology by identifying previously unknown subcellular structures and novel constituents of known cellular organelles.

Characterization of genes expressed in response to cadmium exposure in the earthworm Eisenia fetida using DDRT-PCR

The transition metal cadmium is a pervasive and persistent environmental contaminant that is both a human toxicant and a carcinogen. To inhibit cadmium-induced damage, cells increase the expression of genes encoding stress-response proteins. The transcription of many stress-responsive genes, including those that encode metallothioneins, glutathione-S-transferases (GSTs) and heat shock proteins have been reported. The aim of this work was to investigate in Eisenia fetida the genes whose expressions are regulated following exposure to cadmium. mRNA differential display reverse transcription-polymerase chain reaction was used to analyze gene expression in E. fetida exposed to 50mg/l cadmium solution. Among the derived cDNA clones sequenced, we found 15 genes up-regulated and 12 down-regulated in response to cadmium exposure. The translated amino acid sequences of eight clones were similar to the Lumbricus terrestris hemoglobin dodecamer, Tribolium castaneum membrane protein, Escherichia coli UMN026 DNA-binding transcriptional activator, Brugia malayi immunoglobulin, Homo sapiens cell growth-inhibiting protein, Apis mellifera poly U binding factor, Escherichia fergusonii copper transporter, and the mRNA that encodes E. coli K-12 cytoplasmic insertase into membrane protein. Five cDNA fragments presented no homology with known gene sequences, suggesting that these sequences may either encode proteins not yet identified or correspond to untranslated regions of mRNA molecules. In-depth functional analyses of these genes are needed to reveal their exact roles.

Mitochondrial Lon protease is a human stress protein

The targeted removal of damaged proteins by proteolysis is crucial for cell survival. We have shown previously that the Lon protease selectively degrades oxidized mitochondrial proteins, thus preventing their aggregation and cross-linking. We now show that the Lon protease is a stress-responsive protein that is induced by multiple stressors, including heat shock, serum starvation, and oxidative stress. Lon induction, by pretreatment with low-level stress, protects against oxidative protein damage, diminished mitochondrial function, and loss of cell proliferation induced by toxic levels of hydrogen peroxide. Blocking Lon induction with Lon siRNA also blocks this induced protection. We propose that Lon is a generalized stress-protective enzyme whose decline may contribute to the increased levels of protein damage and mitochondrial dysfunction observed in aging and age-related diseases.

The non-coding RNA gadd7 is a regulator of lipid-induced oxidative and endoplasmic reticulum stress

In obesity and diabetes, an imbalance in fatty acid uptake and fatty acid utilization leads to excess accumulation of lipid in non-adipose tissues. This lipid overload is associated with cellular dysfunction and cell death, which contribute to organ failure, a phenomenon termed lipotoxicity. To elucidate the molecular mechanism of lipid-mediated cell death, we generated and characterized a mutant Chinese hamster ovary cell line that is resistant to palmitate-induced cell death. In this mutant, random insertion of a retroviral promoter trap has disrupted the gene for the non-coding RNA, growth arrested DNA-damage inducible gene 7 (gadd7). Here we report that gadd7 is induced by lipotoxic stress in a reactive oxygen species (ROS)-dependent fashion and is necessary for both lipid- and general oxidative stress-mediated cell death. Depletion of gadd7 by mutagenesis or short hairpin RNA knockdown significantly reduces lipid and non-lipid induced ROS. Furthermore, depletion of gadd7 delays and diminishes ROS-induced endoplasmic reticulum stress. Together these data are the first to implicate a non-coding RNA in a feed-forward loop with oxidative stress and its induction of the endoplasmic reticulum stress response.

Bsr, a nuclear-retained RNA with monoallelic expression

The imprinted Dlk1-Gtl2 and Prader-Willi syndrome (PWS) regions are characterized by a complex noncoding transcription unit spanning arrays of tandemly repeated C/D RNA genes. These noncoding RNAs (ncRNAs) are thought to play an essential but still poorly understood role. To better understand the intracellular fate of these large ncRNAs, fluorescence in situ hybridization was carried out at the rat Dlk1-Gtl2 domain. This locus contains a approximately 100-kb-long gene cluster comprising 86 homologous RBII-36 C/D RNA gene copies, all of them intron-encoded within the ncRNA gene Bsr. Here, we demonstrate that the Bsr gene is monoallelically expressed in primary rat embryonic fibroblasts as well as in hypothalamic neurons and yields a large amount of unspliced and spliced RNAs at the transcription site, mostly as elongated RNA signals. Surprisingly, spliced Bsr RNAs released from the transcription site mainly concentrate as numerous, stable nuclear foci that do not colocalize with any known subnuclear structures. On drug treatments, a fraction of Bsr RNA relocalizes to the cytoplasm and associates with stress granules (SGs), but not with P-bodies, pointing to a potential link between SGs and the metabolism of ncRNA. Thus, Bsr might represent a novel type of nuclear-retained transcript.

Free radical biology and medicine: it's a gas, man!

We review gases that can affect oxidative stress and that themselves may be radicals. We discuss O(2) toxicity, invoking superoxide, hydrogen peroxide, and the hydroxyl radical. We also discuss superoxide dismutase (SOD) and both ground-state, triplet oxygen ((3)O(2)), and the more energetic, reactive singlet oxygen ((1)O(2)). Nitric oxide ((*)NO) is a free radical with cell signaling functions. Besides its role as a vasorelaxant, (*)NO and related species have other functions. Other endogenously produced gases include carbon monoxide (CO), carbon dioxide (CO(2)), and hydrogen sulfide (H(2)S). Like (*)NO, these species impact free radical biochemistry. The coordinated regulation of these species suggests that they all are used in cell signaling. Nitric oxide, nitrogen dioxide, and the carbonate radical (CO(3)(*-)) react selectively at moderate rates with nonradicals, but react fast with a second radical. These reactions establish "cross talk" between reactive oxygen (ROS) and reactive nitrogen species (RNS). Some of these species can react to produce nitrated proteins and nitrolipids. It has been suggested that ozone is formed in vivo. However, the biomarkers that were used to probe for ozone reactions may be formed by non-ozone-dependent reactions. We discuss this fascinating problem in the section on ozone. Very low levels of ROS or RNS may be mitogenic, but very high levels cause an oxidative stress that can result in growth arrest (transient or permanent), apoptosis, or necrosis. Between these extremes, many of the gasses discussed in this review will induce transient adaptive responses in gene expression that enable cells and tissues to survive. Such adaptive mechanisms are thought to be of evolutionary importance.

Identification and characterization of a novel, psoriasis susceptibility-related noncoding RNA gene, PRINS

To identify genetic factors contributing to psoriasis susceptibility, gene expression profiles of uninvolved epidermis from psoriatic patients and epidermis from healthy individuals were compared. Besides already characterized genes, we identified a cDNA with yet unknown functions, which we further characterized and named PRINS (Psoriasis susceptibility-related RNA Gene Induced by Stress). In silico structural and homology studies suggested that PRINS may function as a noncoding RNA. PRINS harbors two Alu elements, it is transcribed by RNA polymerase II, and it is expressed at different levels in various human tissues. Real time reverse transcription-PCR analysis showed that PRINS was expressed higher in the uninvolved epidermis of psoriatic patients compared with both psoriatic lesional and healthy epidermis, suggesting a role for PRINS in psoriasis susceptibility. PRINS is regulated by the proliferation and differentiation state of keratinocytes. Treatment with T-lymphokines, known to precipitate psoriatic symptoms, decreased PRINS expression in the uninvolved psoriatic but not in healthy epidermis. Real time reverse transcription-PCR analysis showed that stress signals such as ultraviolet-B irradiation, viral infection (herpes simplex virus), and translational inhibition increased the RNA level of PRINS. Gene-specific silencing of PRINS by RNA interference revealed that down-regulation of PRINS impairs cell viability after serum starvation but not under normal serum conditions. Our findings suggest that PRINS functions as a noncoding regulatory RNA, playing a protective role in cells exposed to stress. Furthermore, elevated PRINS expression in the epidermis may contribute to psoriasis susceptibility.

Multiple oxidative stress-response members of the Adapt78 family

Adapt78 is an oxidative and calcium stress-response gene. Its protein product is a potent natural inhibitor of the intracellular calcium signaling protein calcineurin. Much of what is known about Adapt78 protein is based on cell-transfection studies. Toward understanding natural endogenous Adapt78, we used an antibody raised against cellular Adapt78 and recently determined that endogenous Adapt78 protein, like its mRNA, is oxidative and calcium stress responsive. Here we report the identification of a second endogenous form of this protein family of 41 kDa. Subcellular fractionation of human HeLa cells revealed that in contrast to results of previous transfection studies, most endogenous Adapt78, characterized as 29 and 41 kDa electrophoretic doublets, resides in the cellular cytosol. The 41 kDa form of Adapt78 was abundant and found to exhibit many characteristics in common with the previously reported oxidative stress-responsive 29 kDa form, including hypo- and hyperphosphorylation variants, rapid loss of the hypophosphorylated form following oxidative stress, response to various kinase and phosphatase inhibitors, and localization. However, it also exhibited some unique characteristics, most notably the lack of calcium inducibility. Finally, the 29 kDa form exhibited a much shorter half-life and strong stabilization following oxidant exposure compared with the 41 kDa Adapt78 form. These data reveal the presence of a novel oxidative stress-responsive 41 kDa Adapt78 species, lend further insight into the Adapt78 family of proteins and their distribution, and challenge previous conclusions obtained using transfection protocols.

Oxidative and calcium stress regulate DSCR1 (Adapt78/MCIP1) protein

DSCR1 (adapt78) is a stress-inducible gene and cytoprotectant. Its protein product, DSCR1 (Adapt78), also referred to as MCIP1, inhibits intracellular calcineurin, a phosphatase that mediates many cellular responses to calcium. Exposure of human U251 and HeLa cells to hydrogen peroxide led to a rapid hyperphosphorylation of DSCR1 (Adapt78). Inhibitor and agonist studies revealed that a broad range of kinases were not responsible for DSCR1 (Adapt78) hyperphosphorylation, including ERK1/2, although parallel activation of the latter was observed. Phosphorylation of both DSCR1 (Adapt78) and ERK1/2 was attenuated by inhibitors of tyrosine phosphatase, suggesting the common upstream involvement of tyrosine dephosphorylation. The hyperphosphorylation electrophoretic shift in DSCR1 (Adapt78) mobility was also observed with other oxidizing agents (peroxynitrite and menadione) but not nonoxidants. Calcium ionophores strongly induced the levels of both hypo- and hyper-phosphorylated DSCR1 (Adapt78) but did not alter phosphorylation status. Calcium-dependent growth factor- and angiotensin II-stimulation also induced both DSCR1 (Adapt78) species. Phosphorylation of either or both serines in a 13-amino acid peptide made to a calcineurin-interacting conserved region of DSCR1 (Adapt78) attenuated inhibition of calcineurin. These data indicate that DSCR1 (Adapt78) protein is a novel, early stage oxidative stress-activated phosphorylation target and newly identified calcium-inducible protein, and suggest that these response mechanisms may contribute to the known cytoprotective and calcineurin-inhibitory activities of DSCR1 (Adapt78).

Non-coding ribonucleic acids--a class of their own?

Non-coding ribonucleic acids (RNAs) do not contain a peptide-encoding open reading frame and are therefore not translated into proteins. They are expressed in all phyla, and in eukaryotic cells they are found in the nucleus, cytoplasm, and mitochondria. Non-coding RNAs either can exert structural functions, as do transfer and ribosomal RNAs, or they can regulate gene expression. Non-coding RNAs with regulatory functions differ in size ranging from a few nucleotides to over 100 kb and have diverse cell- or development-specific functions. Some of the non-coding RNAs associate with human diseases. This chapter summarizes the current knowledge about regulatory non-coding RNAs.

Characterization of adapt33, a stress-inducible riboregulator

We have identified adapt33 as a multiple stress-responsive gene that is induced under conditions of a cytoprotective "adaptive response." adapt33 RNA does not contain any appreciable open reading frame nor produce a protein product and is therefore classified as a stress-inducible riboregulator. Although a number of oxidant stress-modulated, protein-encoding genes have been reported and characterized, very few stress-inducible riboregulator RNAs are known. Here we extend previous studies toward understanding the underlying regulation of expression and function of this rare mammalian riboregulator. mRNA stability and transcription studies determined that adapt33 induction by hydrogen peroxide is at the mRNA stability level, and that adapt33 has a very short half-life. Surprisingly, adapt33 mRNA also exhibits altered electrophoretic migration in response to both hydrogen peroxide and cis-platinum treatment. Although no transcriptional modulation in response to hydrogen peroxide was observed, fusion promoter constructs revealed that adapt33 has an unusually strong promoter that is active in both hamster and human cells. Analysis of expression following the stimulation of apoptosis with hydrogen peroxide and staurosporine revealed a strong correlation with apoptosis, suggesting a possible novel, noncoding RNA component of the apoptotic mechanism. We conclude that adapt33 is a stress-inducible, apoptosis-associated RNA with unique structural and gene promoter characteristics.

Regulation by RNA

In recent years, noncoding RNAs (ncRNAs) have been shown to constitute key elements implicated in a number of regulatory mechanisms in the cell. They are present in bacteria and eukaryotes. The ncRNAs are involved in regulation of expression at both transcriptional and posttranscriptional levels, by mediating chromatin modifications, modulating transcription factor activity, and influencing mRNA stability, processing, and translation. Noncoding RNAs play a key role in genetic imprinting, dosage compensation of X-chromosome-linked genes, and many processes of differentiation and development.

The DSCR1 (Adapt78) isoform 1 protein calcipressin 1 inhibits calcineurin and protects against acute calcium-mediated stress damage, including transient oxidative stress

Although DSCR1 (Adapt78) has been associated with successful adaptation to oxidative stress and calcium stress and with devastating diseases such as Alzheimer's and Down syndrome, no rationale for these apparently contradictory findings has been tested. In fact, DSCR1 (Adapt78) has not yet been proved to provide protection against acute oxidative stress or calcium stress. We have addressed this question using cross-adaptation to H2O2 and the calcium ionophore A23187, stable DSCR1 (Adapt78) transfection and overexpression in hamster HA-1 cells, 'tet-off' regulated DSCR1 (Adapt78) isoform 1 transgene expression in human PC-12 cells, and DSCR1 (Adapt78) antisense oligonucleotides to test the ability of the DSCR1 (Adapt78) protein product calcipressin 1 (a calcineurin inhibitor) to protect against oxidative stress and calcium stress. Under all conditions, resistance to oxidative stress and calcium stress increased as a function of DSCR1 (Adapt78)/calcipressin 1 expression and decreased as gene/protein expression diminished. We conclude that cells may transiently use increased expression of the DSCR1 (Adapt78) gene product calcipressin 1 to provide short-term protection against acute oxidative stress and other calcium-mediated stresses, whereas chronic overexpression may be associated with Alzheimer disease progression.

Maf genes are involved in multiple stress response in human

The Maf protein family consists of eight transcription factors containing a basic-leucine zipper (bZIP) domain. We have previously reported that the mRNA to one of these members, mafG/adapt66, is induced by oxidative stress in hamster HA-1 cells. It has subsequently been reported that mafG is induced bystress that activates the expression of genes under the control of the antioxidant/electrophile response element (ARE/EpRE), and that small Maf proteins are present in ARE/EpRE-protein complexes. Here we extend these studies to assess the effects of various types of stress on maf mRNA induction in human cells. The oxidative stressor cadmium, and the heavy metals cadmium, zinc, and arsenite induced mafG RNA levels within two hours, and maximally at five hours for cadmium and zinc. This induction was observed for multiple transcripts including two not normally associated with mafG, suggesting that these stress agents induced the expression of other related maf family RNAs. Modest induction of mafG mRNA was also observed with heat shock but not calcium elevation. These results suggest that mafG is a human stress-response gene induced by multiple stress, and that several maf (proto-)oncogene members play an important role in cellular stress response.

adapt78 protects cells against stress damage and suppresses cell growth

We have previously identified several genes whose RNA products are induced in HA-1 hamster cells under conditions where a cytoprotective adaptive response is observed. One of these genes, designated adapt78, was found to have a human homolog with some homology to glucose-regulated protein 78 (Grp78). We subsequently determined that adapt78 and grp78 mRNAs are induced by the same stress agents and conclude that adapt78 is a stress-response gene and putative new member of the grp stress gene family. Here we extend these studies to assess the effect of overexpressing adapt78 on stress protection and growth arrest. HA-1 cells stably transfected with adapt78 cDNA were found to exhibit significantly reduced calcium- and hydrogen peroxide-mediated cytotoxicity as compared with control transfectants. In addition, adapt78 stable overexpressors exhibited significantly reduced cell growth. Both cytoprotection and growth arrest accompanied only modest overexpression of adapt78. Flow cytometry revealed that the growth arrest occurred in G(1)-phase. Immunoflourescent analysis revealed that Adapt78 protein exhibits significant perinuclear staining suggestive of endoplasmic reticulum localization in addition to cytoplasmic localization. These data indicate that adapt78 is both cytoprotective and growth suppressive and that these effects may be mediated by Adapt78 protein at the endoplasmic reticulum.

Oxidative stress and gene regulation

Reactive oxygen species are produced by all aerobic cells and are widely believed to play a pivotal role in aging as well as a number of degenerative diseases. The consequences of the generation of oxidants in cells does not appear to be limited to promotion of deleterious effects. Alterations in oxidative metabolism have long been known to occur during differentiation and development. Experimental perturbations in cellular redox state have been shown to exert a strong impact on these processes. The discovery of specific genes and pathways affected by oxidants led to the hypothesis that reactive oxygen species serve as subcellular messengers in gene regulatory and signal transduction pathways. Additionally, antioxidants can activate numerous genes and pathways. The burgeoning growth in the number of pathways shown to be dependent on oxidation or antioxidation has accelerated during the last decade. In the discussion presented here, we provide a tabular summary of many of the redox effects on gene expression and signaling pathways that are currently known to exist.

Polynucleotide degradation during early stage response to oxidative stress is specific to mitochondria

Oxidative stress is known to modulate RNA expression in both prokaryotic and eukaryotic cells. We have previously determined that a preferential and calcium-dependent downregulation of mitochondrial RNA occurs in HA-1 hamster fibroblasts in response to hydrogen peroxide, and that this is accompanied by the degradation of mitochondrial genomic DNA. Here we extended these studies to determine whether downregulation is specific to transcripts derived from mitochondrial-encoded genes; to determine whether genomic DNA degradation occurs in the nucleus; and to compare overall polynucleotide stress response with cellular growth arrest and apoptosis. We observed that nuclear genome-encoded mRNAs whose protein products are targeted for the electron transport chain of mitochondria were not degraded. Furthermore, early stage degradation of genomic DNA, assessed within the first 5 h of peroxide exposure, was specific to mitochondria, as nuclear genomic DNA was not degraded under the same treatment conditions. These differential degradations occurred under conditions where extensive growth-arrest and moderate apoptosis were observed, and were accompanied by significant induction of the growth arrest mRNAs gadd45, gadd153, and adapt15/gadd7. Combined, these results indicate that there is a general degradation of mitochondrial- but not nuclear-polynucleotides during early stage response of HA-1 fibroblasts to oxidative stress.

adapt78, a stress-inducible mRNA, is related to the glucose-regulated protein family of genes

We have recently reported a new oxidant- and calcium-inducible mRNA, adapt78, from hamster HA-1 cells. The adapt78 mRNA is induced in HA-1 cells under conditions where a protective adaptive response is observed and contains a translatable open reading frame whose protein product shows strong homology to a human sequence. Computer analysis of the predicted Adapt78 protein sequence also revealed a stretch of amino acids homologous to a portion of the glucose-regulated protein78 (Grp78). Based on this homology, we tested the hypothesis that adapt78 may be a new member of the grp gene family. Toward this, we assessed the modulation of adapt78 mRNA by stress agents known to induce grp78. In HA-1 cells, adapt78 mRNA was induced by the calcium ionophore A23187, 2-deoxyglucose, brefeldin A, tunicamycin, thapsigargin, and cyclopiazonic acid, with thapsigargin being the most potent inducer (7.3-fold). As expected, grp78 mRNA was also induced by these agents in our model system. In contrast, heat shock treatment produced little if any modulation of either grp78 or adapt78. Differences were also observed, as adapt78 mRNA but not grp78 mRNA was induced by 160 microM hydrogen peroxide, and adapt78 demonstrated earlier induction kinetics for certain agents compared with grp78. adapt78 mRNA was also found to be induced in several different human cell lines. A23187 had the strongest effect on adapt78 mRNA levels in human cells, inducing greater than 20-fold in all human cell cultures tested. Furthermore, in vitro transcription translation of human adapt78 cDNA produced an Adapt78 protein product. We conclude that adapt78 may be a new member of the grp family of genes and may represent an early response grp that complements the actions of grp78 and grp94.

Collection of mRNA-like non-coding RNAs

In last few years much data has accumulated which shows that in different cells various RNA transcripts are synthesized. They lack protein coding capacity and do not produce mature protein. It seems that they work mainly or exclusively on the RNA level. Their function and mechanism of action is poorly understood. In this paper we have collected all known RNA transcript and prepared a database for further structural and functional studies. This is the first collection of the nucleotide sequences of RNAs of this kind. The data can be accessed via WWW at: http://www.man.poznan.pl/5SData/ncRNA/inde x.html

Cadmium-regulated genes from the nematode Caenorhabditis elegans. Identification and cloning of new cadmium-responsive genes by differential display

The transition metal cadmium is a pervasive and persistent environmental contaminant that has been shown to be both a human toxicant and carcinogen. To inhibit cadmium-induced damage, cells respond by increasing the expression of genes encoding stress-response proteins. In most cases, the mechanism by which cadmium affects the expression of these genes remains unknown. It has been demonstrated in several instances that cadmium activates gene transcription through signal transduction pathways, mediated by protein kinase C, cAMP-dependent protein kinase, or calmodulin. A codicil is that cadmium should influence the expression of numerous genes. To investigate the ability of cadmium to affect gene transcription, the differential display technique was used to analyze gene expression in the nematode Caenorhabditis elegans. Forty-nine cDNAs whose steady-state levels of expression change 2-6-fold in response to cadmium exposure were identified. The nucleotide sequences of the majority of the differentially expressed cDNAs are identical to those of C. elegans cosmids, yeast artificial chromosomes, expressed sequence tags, or predicted genes. The translated amino acid sequences of several clones are identical to C. elegans metallothionein-1, HSP70, collagens, and rRNAs. In addition, C. elegans homologues of pyruvate carboxylase, DNA gyrase, beta-adrenergic receptor kinase, and human hypothetical protein KIAA0174 were identified. The translated amino acid sequences of the remaining differentially expressed cDNAs encode novel proteins.

Oxidative stress and superoxide dismutase in development, aging and gene regulation

Free radicals and other reactive oxygen species are produced in the metabolic pathways of aerobic cells and affect a number of biological processes. Oxidation reactions have been postulated to play a role in aging, a number of degenerative diseases, differentiation and development as well as serving as subcellular messengers in gene regulatory and signal transduction pathways. The discovery of the activity of superoxide dismutase is a seminal work in free radical biology, because it established that free radicals were generated by cells and because it made removal of a specific free radical substance possible for the first time, which greatly accelerated research in this area. In this review, the role of reactive oxygen in aging, amyotrophic lateral sclerosis (a neurodegenerative disease), development, differentiation, and signal transduction are discussed. Emphasis is also given to the role of superoxide dismutases in these phenomena.

C-terminal end of v-src protein interacts with peptide coded by gadd7/adapt15-like RNA in two-hybrid system

The significant differences in the metastatic properties of hamster fibroblasts transformed by the Rous sarcoma virus (RSV) were associated with mutations in the v-src carboxy-terminal region. To identify the capacity of this region for protein-protein interaction the two-hybrid system was used. The cDNA clone (vseap1), producing the protein specifically bound with the v-src C-terminal part in yeast cells in vivo and in GST-fusion system in vitro was isolated. Vseap1 shared 68% of homology with stressful agents induced RNA-gadd7/adapt15. Two vseap1 specific messenger RNAs were identified: 0.9-kbp RNA expressed in all transformed cells and three times less in embryo fibroblasts; 3.1-kbp transcript was deleted in the cells with suppressed v-src activity and H2O2 resistance.

Hamster adapt78 mRNA is a Down syndrome critical region homologue that is inducible by oxidative stress

We are using the technique of mRNA differential display to identify RNAs that may be important in protecting cells against the damaging effects of oxidative stress. For these studies, we utilize a so-called "adaptive response" model system in which hamster HA-1 cells respond to a minimally toxic "pretreatment" dose of hydrogen peroxide by synthesizing RNAs and proteins that protect them against subsequent exposure to a highly cytotoxic concentration of hydrogen peroxide. Using this approach, we have recently reported several novel RNAs whose levels are increased under conditions of adaptive response. Here we report a new RNA, designated adapt78, whose steady-state level is significantly induced by a pretreatment dose of hydrogen peroxide. adapt78 mRNA was calculated to be 2.35 kb in size and inducible by the standard pretreatment dose of 4 micromol H2O2/10(7) cells. It was induced as early as 90 min after peroxide exposure and maximally at 5 h. Induction was strongly dependent upon calcium. Cloning and sequencing revealed a large predicted open reading frame of 197 amino acids. In vitro transcription and translation generated a protein of 25,000 Da. GenBank homology analysis revealed that much of adapt78 is strongly homologous to a sequence that has been mapped to the Down syndrome critical region (Fuentes et al., Hum. Mol. Genet. 4, 1935-1944, 1995). However, both the 5' and the 3' ends of adapt78 show no homology to any previously reported complete sequence. adapt78 represents a new oxidant-inducible RNA and marker of cellular oxidative stress and may provide new insight into our understanding of oxidant-related disorders and neural degeneration.

Modulation of a cardiogenic shock inducible RNA by chemical stress: adapt73/PigHep3

BACKGROUND

Understanding how mammalian cells respond to stress is important in the study, detection, and therapy of stress-related disorders. We have been studying cellular stress response in hamster HA-1 cells by using an adaptive response model. HA-1 cells respond to a minimally toxic "pretreatment" dose of hydrogen peroxide by synthesizing RNAs and proteins that protect them against subsequent exposure to a higher cytotoxic concentration of peroxide. The purpose of our studies is to identify and partially characterize any mRNA whose steady state level is significantly modulated during adaptation.

METHODS

HA-1 cells were exposed to a pretreatment dose of hydrogen peroxide and RNA extracted. The differential display technique was used to identify modulated mRNAs. The effects of calcium ionophore A23187 and cis (II)-platinum on the modulation of mRNA from HA-1 cells and A23187 on the modulation of mRNAs from human IMR-90 cells were also determined.

RESULTS

One of the RNAs induced by a pretreatment concentration of hydrogen peroxide was designated adapt73. The size of the induced adapt73 RNA was determined to be 2.1 kb. Induction of adapt73 was maximal 5 hours after peroxide treatment, but elevated levels were still obvious at 10 hours. This induction was not specific to oxidative stress, because other stress agents including as (II)-platinum and especially calcium ionophore A23187 also induced adapt73 mRNA levels. Partial sequencing of adapt73 and a subsequent GenBank homology search revealed extensive homology to a novel RNA from pig, designated PigHep3, that was identified as a cardiogenic shock response gene from liver in pigs that were undergoing resuscitation after circulatory shock. Homology to a completely sequenced but uncharacterized human homolog was also found. Using a partially sequenced expressed sequence tag (EST) human clone to adapt73, we probed Northern blots containing RNA from IMR-90 human fibroblasts treated with A23187. A strongly induced human adapt73 mRNA homolog was observed, almost identical in size to its hamster homolog. In vitro transcription and translation of the human EST clone revealed a translatable Adapt73 protein product.

CONCLUSIONS

These data indicate that adapt73/PigHep3 RNA can be induced by multiple chemical stress, that these inductions occur under protective or adaptive response conditions, that there is an inducible human homolog to adapt73, and suggest that adapt73 may be an important physiologic mediator of organ and cellular shock response in mammals.

16S mitochondrial ribosomal RNA degradation is associated with apoptosis

The use of mitochondrial RNA as an indicator of apoptosis was investigated. Exposure of HA-1 fibroblastic cells to 10 micromol H(2)O(2) per 10(7) cells induced nuclear fragmentation, cell shrinkage, and internucleosomal DNA fragmentation, all characteristics of apoptosis. RNA extracted from control and apoptotic cultures, and analyzed by Northern blot hybridization, revealed a significant increase in the degradation of mitochondrial 16S ribosomal RNA (rRNA) that was associated with apoptosis. Conversely, minimal, if any, degradation of glyceraldehyde-3-phosphate dehydrogenase or actin mRNAs was observed. Similar results were obtained for HA-1 cells treated with the protein kinase inhibitor staurosporine, and for HT-2 T-lymphocytes induced to undergo apoptosis by interleukin-2 withdrawal. In addition, 16S rRNA degradation was an early event that was discernable well before chromatin condensation in hydrogen peroxide-treated HA-1 cells. These observations suggest that degradation of mitochondrial 16S ribosomal RNA is a new marker of mammalian cell apoptosis.

Down-regulation of mammalian mitochondrial RNAs during oxidative stress

We have identified an RNA species that appears to be induced by oxidative stress in hamster HA-1 fibroblasts using the differential display technique, but instead is found to be degraded when evaluated by Northern blot hybridization. Cloning and subsequent sequencing identified the partially degraded RNA as 16S ribosomal RNA (rRNA), a major component of mitochondrial ribosomes. Degradation, and associated decreases in the levels of the mature- and precursor-species of 16S rRNA, appear to be dependent upon calcium, but not cytoplasmic protein synthesis nor nuclear transcription. Other decreased mitochondrial RNAs were also identified, including 12S rRNA, NADH dehydrogenase subunit 6, ATPase subunit 6, and cytochrome oxidase subunits I and III. A significant part of many, if not all, of these RNA decreases was due to degradation. As compared with 16S rRNA, significantly less degradation was observed for cytoplasmic 28S/18S rRNAs, even at very high peroxide concentration. Analysis of 21 cytoplasmic mRNAs revealed little or no decrease in mature band signal in response to peroxide, and several cytoplasmic mRNAs were actually up-regulated. Thus, a preferential down-regulation of mitochondrial RNAs occurs in HA-1 fibroblasts in response to hydrogen peroxide. Subcellular fractionation analysis, using 16S rRNA degradation as a gauge, indicates that this down-regulation is specific to mitochondria. The down-regulation of mitochondrial RNAs may represent a general mechanism by which cells protect themselves against oxidative stress.

Oxidative stress induces the levels of a MafG homolog in hamster HA-1 cells

The Maf family encodes nuclear proteins that recognize AP-1-like response elements. MafB, MafK, MafF, and MafG, are all able to heterodimerize with each other, c-fos, and erythroid cell-specific transcription factor NF-E2, to affect the transcription of target genes. Using the technique of differential display, we recently identified a new oxidant-inducible mRNA, designated adapt66, in HA-1 hamster fibroblasts. Cloning, partial sequencing, and GenBank analysis of adapt66 revealed strong homology to chicken mafG, a newly identified member of the maf oncogene family. The mafG homolog/adapt66 mRNA induction appeared to be dependent upon calcium; occurred as early as 90 minutes following exposure of HA-1 cells to hydrogen peroxide; and peaked between 5 and 10 hours after peroxide treatment. It has previously been demonstrated that several cellular transcription factors, including Fos, can be induced by oxidative stress. The induction of the DNA binding sequence mafG homolog/adapt66 by hydrogen peroxide, and it's known interaction with c-fos, may represent important mechanisms by which oxidative stress can modulate gene expression.