The eukaryote chaperonin CCT is a cold shock protein in Saccharomyces cerevisiae

Comparative Population Transcriptomics Provide New Insight into the Evolutionary History and Adaptive Potential of World Ocean Krill

Genetic variation is instrumental for adaptation to changing environments but it is unclear how it is structured and contributes to adaptation in pelagic species lacking clear barriers to gene flow. Here, we applied comparative genomics to extensive transcriptome datasets from 20 krill species collected across the Atlantic, Indian, Pacific, and Southern Oceans. We compared genetic variation both within and between species to elucidate their evolutionary history and genomic bases of adaptation. We resolved phylogenetic interrelationships and uncovered genomic evidence to elevate the cryptic Euphausia similis var. armata into species. Levels of genetic variation and rates of adaptive protein evolution vary widely. Species endemic to the cold Southern Ocean, such as the Antarctic krill Euphausia superba, showed less genetic variation and lower evolutionary rates than other species. This could suggest a low adaptive potential to rapid climate change. We uncovered hundreds of candidate genes with signatures of adaptive evolution among Antarctic Euphausia but did not observe strong evidence of adaptive convergence with the predominantly Arctic Thysanoessa. We instead identified candidates for cold-adaptation that have also been detected in Antarctic fish, including genes that govern thermal reception such as TrpA1. Our results suggest parallel genetic responses to similar selection pressures across Antarctic taxa and provide new insights into the adaptive potential of important zooplankton already affected by climate change.

Integrated Analysis of DNA Methylome and Transcriptome Reveals Epigenetic Regulation of Cold Tolerance in Litopenaeus vannamei

DNA methylation is an important epigenetic modification that has been shown to be associated with responses to non-biological stressors. However, there is currently no research on DNA methylation in response to environmental signals in shrimp. In this study, we conducted a comprehensive comparative analysis of DNA methylation profiles and differentially expressed genes between two strains of Litopenaeus vannamei with significantly different cold tolerance through whole genome bisulfite sequencing (WGBS) and transcriptome sequencing. Between Lv-C and Lv-T (constant temperature of 28 °C and low temperatures of 18 °C and 10 °C) under cytosine-guanine (CG) environments, 39,100 differentially methylated regions (DMRs) were identified, corresponding to 9302 DMR-related genes (DMRGs). The DMRs were mainly located in the gene body (exons and introns). Gene Ontology (GO) analysis showed that these DMRGs were significantly enriched in cell parts, catalytic activity, and metabolic processes. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed significant enrichment of these DMRGs in pathways such as proteasome (ko03050), oxidative phosphorylation (ko00190), mTOR signaling pathway (ko04150), fatty acid metabolism (ko01212), and fatty acid degradation (ko00071). The comprehensive results suggested that L. vannamei mainly regulates gene expression in response to low temperatures through hypermethylation or demethylation of some genes involved in thermogenesis, glycolysis, the autophagy pathway, the peroxisome, and drug metabolism pathways. These results provide important clues for studying DNA methylation patterns and identifying cold tolerance genes in shrimp.

The potential of cold-shock promoters for the expression of recombinant proteins in microbes and mammalian cells

BACKGROUND

Low-temperature expression of recombinant proteins may be advantageous to support their proper folding and preserve bioactivity. The generation of expression vectors regulated under cold conditions can improve the expression of some target proteins that are difficult to express in different expression systems. The cspA encodes the major cold-shock protein from Escherichia coli (CspA). The promoter of cspA has been widely used to develop cold shock-inducible expression platforms in E. coli. Moreover, it is often necessary to employ expression systems other than bacteria, particularly when recombinant proteins require complex post-translational modifications. Currently, there are no commercial platforms available for expressing target genes by cold shock in eukaryotic cells. Consequently, genetic elements that respond to cold shock offer the possibility of developing novel cold-inducible expression platforms, particularly suitable for yeasts, and mammalian cells.

CONCLUSIONS

This review covers the importance of the cellular response to low temperatures and the prospective use of cold-sensitive promoters to direct the expression of recombinant proteins. This concept may contribute to renewing interest in applying white technologies to produce recombinant proteins that are difficult to express.

The intrinsic chaperone network of Arabidopsis stem cells confers protection against proteotoxic stress

The biological purpose of plant stem cells is to maintain themselves while providing new pools of differentiated cells that form organs and rejuvenate or replace damaged tissues. Protein homeostasis or proteostasis is required for cell function and viability. However, the link between proteostasis and plant stem cell identity remains unknown. In contrast to their differentiated counterparts, we find that root stem cells can prevent the accumulation of aggregated proteins even under proteotoxic stress conditions such as heat stress or proteasome inhibition. Notably, root stem cells exhibit enhanced expression of distinct chaperones that maintain proteome integrity. Particularly, intrinsic high levels of the T-complex protein-1 ring complex/chaperonin containing TCP1 (TRiC/CCT) complex determine stem cell maintenance and their remarkable ability to suppress protein aggregation. Overexpression of CCT8, a key activator of TRiC/CCT assembly, is sufficient to ameliorate protein aggregation in differentiated cells and confer resistance to proteotoxic stress in plants. Taken together, our results indicate that enhanced proteostasis mechanisms in stem cells could be an important requirement for plants to persist under extreme environmental conditions and reach extreme long ages. Thus, proteostasis of stem cells can provide insights to design and breed plants tolerant to environmental challenges caused by the climate change.

Convergent Evolution and Structural Adaptation to the Deep Ocean in the Protein-Folding Chaperonin CCTα

The deep ocean is the largest biome on Earth and yet it is among the least studied environments of our planet. Life at great depths requires several specific adaptations; however, their molecular mechanisms remain understudied. We examined patterns of positive selection in 416 genes from four brittle star (Ophiuroidea) families displaying replicated events of deep-sea colonization (288 individuals from 216 species). We found consistent signatures of molecular convergence in functions related to protein biogenesis, including protein folding and translation. Five genes were recurrently positively selected, including chaperonin-containing TCP-1 subunit α (CCTα), which is essential for protein folding. Molecular convergence was detected at the functional and gene levels but not at the amino-acid level. Pressure-adapted proteins are expected to display higher stability to counteract the effects of denaturation. We thus examined in silico local protein stability of CCTα across the ophiuroid tree of life (967 individuals from 725 species) in a phylogenetically corrected context and found that deep-sea-adapted proteins display higher stability within and next to the substrate-binding region, which was confirmed by in silico global protein stability analyses. This suggests that CCTα displays not only structural but also functional adaptations to deep-water conditions. The CCT complex is involved in the folding of ∼10% of newly synthesized proteins and has previously been categorized as a "cold-shock" protein in numerous eukaryotes. We thus propose that adaptation mechanisms to cold and deep-sea environments may be linked and highlight that efficient protein biogenesis, including protein folding and translation, is a key metabolic deep-sea adaptation.

Unveiling Kiwifruit Metabolite and Protein Changes in the Course of Postharvest Cold Storage

Actinidia deliciosa cv. Hayward fruit is renowned for its micro- and macronutrients, which vary in their levels during berry physiological development and postharvest processing. In this context, we have recently described metabolic pathways/molecular effectors in fruit outer endocarp characterizing the different stages of berry physiological maturation. Here, we report on the kiwifruit postharvest phase through an integrated approach consisting of pomological analysis combined with NMR/LC-UV/ESI-IT-MSn- and 2D-DIGE/nanoLC-ESI-LIT-MS/MS-based proteometabolomic measurements. Kiwifruit samples stored under conventional, cold-based postharvest conditions not involving the use of dedicated chemicals were sampled at four stages (from fruit harvest to pre-commercialization) and analyzed in comparison for pomological features, and outer endocarp metabolite and protein content. About 42 metabolites were quantified, together with corresponding proteomic changes. Proteomics showed that proteins associated with disease/defense, energy, protein destination/storage, cell structure and metabolism functions were affected at precise fruit postharvest times, providing a justification to corresponding pomological/metabolite content characteristics. Bioinformatic analysis of variably represented proteins revealed a central network of interacting species, modulating metabolite level variations during postharvest fruit storage. Kiwifruit allergens were also quantified, demonstrating in some cases their highest levels at the fruit pre-commercialization stage. By lining up kiwifruit postharvest processing to a proteometabolomic depiction, this study integrates previous observations on metabolite and protein content in postharvest berries treated with specific chemical additives, and provides a reference framework for further studies on the optimization of fruit storage before its commercialization.

Elevated chaperone proteins are a feature of winter freeze avoidance by larvae of the goldenrod gall moth, Epiblema scudderiana

Winter survival for many insect species includes a need to maintain metabolic homeostasis and structural/functional integrity of macromolecules not only over a wide range of cold temperatures but also in response to rapid temperature change. Chaperones are well-known to protect/stabilize protein structure with regard to heat stress but less is known about their potential involvement in long-term protection of the proteome at subzero temperatures. The present study assessed the participation of chaperone proteins in the cold hardiness of larvae of the goldenrod gall moth, Epiblema scudderiana (Clemens) (Lepidoptera, Olethreutidae), monitoring changes in nine proteins over the winter months as well as their responses to laboratory cold acclimation or anoxia exposure. Four heat shock proteins (HSPs: Hsp110, Hsp70, Hsp60, Hsp40), three glucose-regulated proteins (GRPs: Grp78, Grp 94, Grp170) and the tailless complex polypeptide 1 (TCP-1) as well as the heat shock transcription factor (HSF1) were investigated. In general, all were significantly elevated in larvae collected from an outdoor site between October and March, as compared with September values, and chaperone levels were reduced again in April. The October to March interval also includes the period of diapause followed by cold quiescence in the species. Relative expression of Hsp70, Hsp60 and Hsp40 rose by 2-3-fold, GRPs increased 1.5-3-fold, and levels of active (hyperphosphorylated) HSF1 increased by 4-4.8-fold over the midwinter months. Chilling from 15°C to 4°C in the laboratory upregulated Grp78 protein content that remained high as temperature was further reduced to -4°C and then -20°C whereas Hsp110, Hsp70 and HSF1 levels increased when larvae were exposed to -4°C and -20°C. Grp170 (also known as oxygen-regulated protein 150) was the only chaperone that increased significantly in the larvae in response to anoxia exposure at 4°C. The data also indicated that multiple subcellular compartments received enhanced protection for their proteome since upregulation of chaperones included proteins known to occur in cytosolic (Hsp40, Hsp70), mitochondrial (Hsp60) and endoplasmic reticulum (Grp170) locations. Overall, the data indicate that chaperones have a significant role to play in the winter cold hardiness of E. scudderiana and identify declining temperatures (and perhaps also oxygen restriction) as potential modulators of chaperone production. The data add support to a relatively understudied area of insect cold hardiness - the long-term protection and stabilization of the proteome over the winter months.

Autolysis of Pichia pastoris induced by cold

The production of recombinant biopharmaceutical proteins is a multi-billion dollar market. Protein recovery represents a major part of the production costs. Pichia pastoris is one of the microbial systems most used for the production of heterologous proteins. The use of a cold-induced promoter to express lytic enzymes in the yeast after the growth stage could reduce protein recovery costs. This study shows that a cold-shock can be applied to induce lysis of the yeast cells. A strain of P. pastoris was constructed in which the endogenous eng gene encoding a putative endo-β-1,3-glucanase was overexpressed using the cold-shock induced promoter of the cctα gene from Saccharomyces cerevisiae. In the transgenic P. pastoris, the expression of eng increased 3.6-fold after chilling the cells from 30 to 4 °C (cold-shock stage) followed by incubation for 6 h (eng expression stage). The culture was heated to 30 °C for 6 h (ENG synthesis stage) and kept at 37 °C for 24 h (lysis stage). After this procedure the cell morphology changed, spheroplasts were obtained and cellular lysis was observed. Thus, a clone of P. pastoris was obtained, which undergoes autolysis after a cold-shock.

Evolutionary genomics of Culex pipiens: global and local adaptations associated with climate, life-history traits and anthropogenic factors

We present the first genome-wide study of recent evolution in Culex pipiens species complex focusing on the genomic extent, functional targets and likely causes of global and local adaptations. We resequenced pooled samples of six populations of C. pipiens and two populations of the outgroup Culex torrentium. We used principal component analysis to systematically study differential natural selection across populations and developed a phylogenetic scanning method to analyse admixture without haplotype data. We found evidence for the prominent role of geographical distribution in shaping population structure and specifying patterns of genomic selection. Multiple adaptive events, involving genes implicated with autogeny, diapause and insecticide resistance were limited to specific populations. We estimate that about 5–20% of the genes (including several histone genes) and almost half of the annotated pathways were undergoing selective sweeps in each population. The high occurrence of sweeps in non-genic regions and in chromatin remodelling genes indicated the adaptive importance of gene expression changes. We hypothesize that global adaptive processes in the C. pipiens complex are potentially associated with South to North range expansion, requiring adjustments in chromatin conformation. Strong local signature of adaptation and emergence of hybrid bridge vectors necessitate genomic assessment of populations before specifying control agents.

Characterization of CCTα and evaluating its expression in the mud crab Scylla paramamosain when challenged by low temperatures alone and in combination with high and low salinity

Chaperonin containing the T-complex polypeptide-1 (CCT), which is known to be involved in intracellular assembly and folding of proteins, is a class of chaperonin omnipresent in all forms of life. Previous studies showed that CCT played a vital role in cold hardiness of various animals. In order to understand the response of the polypeptide complex to low temperature challenge and other environmental stresses, a subunit of CCT (CCTα) was cloned from the mud crab Scylla paramamosain by expressed sequence tag (EST) analysis and rapid amplification of cDNA ends (RACE). The full-length cDNA SpCCTα was of 1972 bp and contained a 1668 bp open reading frame (ORF) encoding a polypeptide of 555 amino acids with four conserved motifs. The messenger ribonucleic acid (mRNA) levels of SpCCTα in ten tissues of adult S. paramamosain was subsequently examined and the highest expression was found in muscle, followed by gill, hepatopancreas, thoracic ganglion, hemocyte, heart, cerebral ganglion, stomach, eyestalk ganglion, and epidermis. The expressions of SpCCTα in the muscle of sub-adult crabs (pre-acclimated to 28 °C) subjected to the challenges of both lower temperatures (25, 20, 15, and 10 °C) alone and low temperatures (15 and 10 °C) in combination with salinity of 35 and 10 were further investigated by fluorescent quantitative real-time PCR (qPCR). It was revealed that when exposed to lower temperatures alone, the mRNA transcripts of the SpCCTα gene in the muscle were generally induced for significant higher expression at 10 °C treatment than the 25, 20, and 15 °C treatments; meanwhile, exposure to 15 °C also frequently led to significantly higher expression than those at 20 and 25 °C. This finding indicated that the up-regulation of SpCCTα was closely related to the cold hardiness of S. paramamosain. The results of an additional experiment challenging the sub-adult crabs with various combinations of low temperatures with different salinity conditions generally demonstrated that at both 10 and 15 °C, the expression of SpCCTα under the high salinity of 35 was significantly lower than that at low salinity of 10, implying that the damages caused by low temperatures with high salinity were less than that under low salinity.

Gpd1 Regulates the Activity of Tcp-1 and Heat Shock Response in Yeast Cells: Effect on Aggregation of Mutant Huntingtin

A significant correlation has been observed between the length of the polyglutamine tract in huntingtin, its aggregation and the progression of Huntington's disease (HD). The chaperonin TRiC is a potent antagonist of aggregation of mutant huntingtin. Using the well-validated Saccharomyces cerevisiae model of HD, we have investigated the role of age-related post-translational modifications of this heterooligomeric chaperonin on its ability to inhibit aggregation of the mutant protein. We show that the glycerol synthetic enzyme Gpd1 is involved in the post-translational modification of Tcp-1 (subunit of TRiC) by acetylation and glycation through the NAD(+)/NADH shuttle and the triose phosphate intermediate dihydroxyacetone phosphate, respectively. The extent of modification of Tcp-1 shows a negative correlation with the solubility of mutant huntingtin. The absence of Gpd1 also induces heat shock response in yeast cells, further inhibiting aggregation of the mutant protein. Thus, Gpd1 acts as a major regulator of the protein folding machinery in the yeast model of HD. Modification and inactivation of cellular chaperonin are accelerated in an aging cell, which has further deleterious effects for a cell harbouring misfolded/aggregated protein(s).

From Glacier to Sauna: RNA-Seq of the Human Pathogen Black Fungus Exophiala dermatitidis under Varying Temperature Conditions Exhibits Common and Novel Fungal Response

Exophiala dermatitidis (Wangiella dermatitidis) belongs to the group of the so-called black yeasts. Thanks in part to its thick and strongly melanized cell walls, E. dermatitidis is extremely tolerant to various kinds of stress, including extreme pH, temperature and desiccation. E. dermatitidis is also the agent responsible for various severe illnesses in humans, such as pneumonia and keratitis, and might lead to fatal brain infections. Due to its association with the human environment, its poly-extremophilic lifestyle and its pathogenicity in humans, E. dermatitidis has become an important model organism. In this study we present the functional analysis of the transcriptional response of the fungus at 1°C and 45°C, in comparison with that at 37°C, for two different exposition times, i.e. 1 hour and 1 week. At 1°C, E. dermatitidis uses a large repertoire of tools to acclimatize, such as lipid membrane fluidization, trehalose production or cytoskeleton rearrangement, which allows the fungus to remain metabolically active. At 45°C, the fungus drifts into a replicative state and increases the activity of the Golgi apparatus. As a novel finding, our study provides evidence that, apart from the protein coding genes, non-coding RNAs, circular RNAs as well as fusion-transcripts are differentially regulated and that the function of the fusion-transcripts can be related to the corresponding temperature condition. This work establishes that E. dermatitidis adapts to its environment by modulating coding and non-coding gene transcription levels and through the regulation of chimeric and circular RNAs.

Biology of the heat shock response and protein chaperones: budding yeast (Saccharomyces cerevisiae) as a model system

The eukaryotic heat shock response is an ancient and highly conserved transcriptional program that results in the immediate synthesis of a battery of cytoprotective genes in the presence of thermal and other environmental stresses. Many of these genes encode molecular chaperones, powerful protein remodelers with the capacity to shield, fold, or unfold substrates in a context-dependent manner. The budding yeast Saccharomyces cerevisiae continues to be an invaluable model for driving the discovery of regulatory features of this fundamental stress response. In addition, budding yeast has been an outstanding model system to elucidate the cell biology of protein chaperones and their organization into functional networks. In this review, we evaluate our understanding of the multifaceted response to heat shock. In addition, the chaperone complement of the cytosol is compared to those of mitochondria and the endoplasmic reticulum, organelles with their own unique protein homeostasis milieus. Finally, we examine recent advances in the understanding of the roles of protein chaperones and the heat shock response in pathogenic fungi, which is being accelerated by the wealth of information gained for budding yeast.

Chaperone proteins and winter survival by a freeze tolerant insect

The role of chaperone proteins in the winter survival of insects was evaluated in freeze tolerant gall fly larvae, Eurosta solidaginis. Levels of four heat shock proteins (Hsp110, Hsp70, Hsp60, Hsp40), two glucose-regulated proteins (Grp75, Grp78) and three others (tailless complex polypeptide 1 [TCP-1], αA-crystallin, αB-crystallin) were tracked in outdoor larvae from September to April and, in addition, laboratory experiments assessed chilling, freezing, and anoxia effects on these proteins. Gall fly larvae showed consistent elevation of Hsp110, Hsp70, Hsp40, Grp78 and αB-crystallin over the late autumn and winter months, generally 1.5-2.0-fold higher than September values. This suggests that these proteins contribute to cell preservation over the winter months via protection and stabilization of macromolecules. By contrast, levels of the mitochondrial Hsp60 fell to just 40% of September values by midwinter, paralleling the responses by numerous mitochondrial enzymes and consistent with a reduction in total mitochondria numbers over the winter. None of the proteins were altered when 15°C acclimated larvae were chilled to 3°C for 24h but Hsp70, Hsp40 and Grp75 increased during freezing at -16°C for 24h whereas others (Hsp110, TCP-1 and both crystallins) increased significantly after larvae thawed at 3°C. Anoxia exposure (24h under N2 gas at 15°C) elevated levels of Hsp70, Grp78 and the two crystallins. Levels of active hyperphosphorylated heat shock transcription factor (HSF1) were also analyzed, giving an indication of the state of hsp gene transcription in the larvae. HSF1 was high in September and October but fell to less than 40% of September values in midwinter consistent with suppression of gene transcription in diapause larvae. HSF1 levels responded positively to freezing and increased robustly by 4.9-fold under anoxia. Overall, the data provide strong evidence for the importance of protein chaperones as a mechanism of cell preservation in freeze tolerant insects.

Isolation of diapause-regulated genes from the flesh fly, Sarcophaga crassipalpis by suppressive subtractive hybridization

Subtractive suppressive hybridization (SSH) was used to characterize the diapause transcriptome of the flesh fly Sarcophaga crassipalpis. Through these efforts, we isolated 97 unique clones which were used as probes in northern hybridization to assess their expression during diapause. Of these, 17 were confirmed to be diapause upregulated and 1 was diapause downregulated, while 12 were shown to be unaffected by diapause in this species. The diapause upregulated genes fall into several broad categories including heat shock proteins, heavy metal responsive genes, neuropeptides, structural genes, regulatory elements, and several genes of unknown function. In combination with other large-scale analyses of gene expression during diapause, this study assists in the characterization of the S. crassipalpis diapause transcriptome, and begins to identify common elements involved in diapause across diverse taxa.

Chaperonin contributes to cold hardiness of the onion maggot Delia antiqua through repression of depolymerization of actin at low temperatures

Winter-diapause and cold-acclimated non-diapause pupae of the onion maggot, Delia antiqua (Diptera: Anthomyiidae), show strong cold hardiness. To obtain insights into the mechanisms involved in the enhancement of cold hardiness, we investigated the expression patterns of genes encoding subunits of chaperonin (CCT) and the morphology of actin, a substrate of CCT, at low temperatures. Quantitative real-time PCR analyses showed the mRNA levels of CCT subunits in pupal tissues to be highly correlated with the cold hardiness of the pupae. While actin in the Malpighian tubules of non-cold-hardy pupae showed extensive depolymerization after a cold treatment, actin in the same tissue of cold-hardy pupae was not depolymerized. Damage to cell membranes became apparent after the depolymerization of actin. Moreover, administration of Latrunculin B, an inhibitor of actin polymerization, to the larvae markedly decreased the cold hardiness of the pupae obtained. These findings suggest that CCT contributes to the cold hardiness of D. antiqua through the repression of depolymerization of actin at low temperatures.

Up-regulation of heat shock proteins is essential for cold survival during insect diapause

Diapause, the dormancy common to overwintering insects, evokes a unique pattern of gene expression. In the flesh fly, most, but not all, of the fly's heat shock proteins (Hsps) are up-regulated. The diapause up-regulated Hsps include two members of the Hsp70 family, one member of the Hsp60 family (TCP-1), at least four members of the small Hsp family, and a small Hsp pseudogene. Expression of an Hsp70 cognate, Hsc70, is uninfluenced by diapause, and Hsp90 is actually down-regulated during diapause, thus diapause differs from common stress responses that elicit synchronous up-regulation of all Hsps. Up-regulation of the Hsps begins at the onset of diapause, persists throughout the overwintering period, and ceases within hours after the fly receives the signal to reinitiate development. The up-regulation of Hsps appears to be common to diapause in species representing diverse insect orders including Diptera, Lepidoptera, Coleoptera, and Hymenoptera as well as in diapauses that occur in different developmental stages (embryo, larva, pupa, adult). Suppressing expression of Hsp23 and Hsp70 in flies by using RNAi did not alter the decision to enter diapause or the duration of diapause, but it had a profound effect on the pupa's ability to survive low temperatures. We thus propose that up-regulation of Hsps during diapause is a major factor contributing to cold-hardiness of overwintering insects.

Control and regulation of the cellular responses to cold shock: the responses in yeast and mammalian systems

Although the cold-shock response has now been studied in a number of different organisms for several decades, it is only in the last few years that we have begun to understand the molecular mechanisms that govern adaptation to cold stress. Notably, all organisms from prokaryotes to plants and higher eukaryotes respond to cold shock in a comparatively similar manner. The general response of cells to cold stress is the elite and rapid overexpression of a small group of proteins, the so-called CSPs (cold-shock proteins). The most well characterized CSP is CspA, the major CSP expressed in Escherichia coli upon temperature downshift. More recently, a number of reports have shown that exposing yeast or mammalian cells to sub-physiological temperatures (<30 or <37 degrees C respectively) invokes a co-ordinated cellular response involving modulation of transcription, translation, metabolism, the cell cycle and the cell cytoskeleton. In the present review, we summarize the regulation and role of cold-shock genes and proteins in the adaptive response upon decreased temperature with particular reference to yeast and in vitro cultured mammalian cells. Finally, we present an integrated model for the co-ordinated responses required to maintain the viability and integrity of mammalian cells upon mild hypothermic cold shock.

The cold-shock response in cultured mammalian cells: harnessing the response for the improvement of recombinant protein production

There are a growing number of reports on the sub-physiological temperature culturing (<37 degrees C) of mammalian cells for increased recombinant protein yield, although the effect is variable between cell lines, expression systems, and the product of interest. What is becoming clear is that exposing mammalian cells to sub-physiological temperatures invokes a coordinated cellular response involving modulation of the cell cycle, metabolism, transcription, translation, and the cell cytoskeleton. Opportunities currently exist for further enhancement of the cold-shock effect on recombinant protein production in mammalian cells through advancements in our understanding of the mechanisms involved in the cold-shock response.

Heat shock response of Archaeoglobus fulgidus

The heat shock response of the hyperthermophilic archaeon Archaeoglobus fulgidus strain VC-16 was studied using whole-genome microarrays. On the basis of the resulting expression profiles, approximately 350 of the 2,410 open reading frames (ORFs) (ca. 14%) exhibited increased or decreased transcript abundance. These span a range of cell functions, including energy production, amino acid metabolism, and signal transduction, where the majority are uncharacterized. One ORF called AF1298 was identified that contains a putative helix-turn-helix DNA binding motif. The gene product, HSR1, was expressed and purified from Escherichia coli and was used to characterize specific DNA recognition regions upstream of two A. fulgidus genes, AF1298 and AF1971. The results indicate that AF1298 is autoregulated and is part of an operon with two downstream genes that encode a small heat shock protein, Hsp20, and cdc48, an AAA+ ATPase. The DNase I footprints using HSR1 suggest the presence of a cis-binding motif upstream of AF1298 consisting of CTAAC-N5-GTTAG. Since AF1298 is negatively regulated in response to heat shock and encodes a protein only distantly related to the N-terminal DNA binding domain of Phr of Pyrococcus furiosus, these results suggest that HSR1 and Phr may belong to an evolutionarily diverse protein family involved in heat shock regulation in hyperthermophilic and mesophilic Archaea organisms.

Expression of mRNA for the t-complex polypeptide-1, a subunit of chaperonin CCT, is upregulated in association with increased cold hardiness in Delia antiqua

Summer-diapause and winter-diapause pupae of the onion maggot, Delia antiqua (Diptera: Anthomyiidae), were significantly more cold hardy than nondiapause, prediapause, and postdiapause pupae. Moreover, cold acclimation of nondiapause pupae conferred strong cold hardiness comparable with that of diapause pupae. Differential display analysis revealed that the expression of a gene encoding TCP-1 (the t-complex polypeptide-1), a subunit of chaperonin CCT, in D antiqua (DaTCP-1) is upregulated in the pupae that express enhanced cold hardiness. Quantitative real-time polymerase chain reaction analyses showed that the levels of DaTCP-1 messenger RNA in pupal tissues, brain, and midgut in particular, are highly correlated with the cold hardiness of the pupae. These findings suggest that the upregulation of DaTCP-1 expression is related to enhanced cold hardiness in D antiqua. The upregulation of CCT in response to low temperature in an organism other than the yeast is newly reported.

Yeast gene expression during growth at low temperature

Gene expression during growth at low temperature in the yeast Saccharomyces cerevisiae was investigated by means of DNA microarray analysis. A large number of genes showed an increase or decrease in expression at 4 degrees C relative to 25 degrees C. Although a temperature shift was not performed, differential expression of the cold shock genes TIP1, TIR1, TIR2, and NSR1 was observed. These genes may be necessary for growth at temperatures as low as 4 degrees C as well as for adapting to rapid drops in temperature. A new class of genes, many with unknown functions, was found to be induced during growth at low temperature. We propose to call these genes "low temperature growth genes."

Function and regulation of cytosolic molecular chaperone CCT

Molecular chaperones are a group of proteins that assists in the folding of newly synthesized proteins or in the refolding of denatured proteins. The cytosolic chaperonin-containing t-complex polypeptide 1 (CCT) is a molecular chaperone that plays an important role in the folding of proteins in the eukaryotic cytosol. Actin, tubulin, and several other proteins are known to be folded by CCT, and an estimated 15% of newly translated proteins in mammalian cells are folded with the assistance of CCT. CCT differs from other chaperonin family proteins in its subunit composition, which consists of eight subunit species comprising the CCT 16-mer double-ring-like complex. CCT preferentially recognizes quasinative (or partially folded) intermediates, whereas its Escherichia coli homologue GroEL recognizes more unfolded intermediates, especially those displaying hydrophobic surfaces. Molecular evolutionary analyses have suggested that each subunit species has a specific function in addition to contributing to a common ATPase activity. Consistent with this view, it has been suggested that each subunit recognizes specific substrate proteins (or their parts) and that they collectively modulate the ATPase activity of the complex. The overall expression of CCT in mammalian cells is primarily dependent on cell growth, but each subunit exhibits an individual patterns of expression. Recent progress in CCT research is reviewed, focusing particularly on CCT function and expression. From these observations, the possible roles of the distinct subunits in CCT-assisted folding in the eukaryotic cytosol are discussed.