Locus encoding a family of small heat shock genes in Caenorhabditis elegans: two genes duplicated to form a 3.8-kilobase inverted repeat

A simple strategy for addition of degron tags to endogenous genes harboring prior insertions of fluorescent protein

There exist insufficient validated "entry portal" sites in the C. elegans genome for CRISPR/Cas9-dependent insertion into endogenous genes to confer diverse spatiotemporal patterns and levels of expression on exogenous sequences. Consequently, we recognized the most common potential "entry portal" sequences: genes previously tagged with fluorescent proteins using CRISPR/Cas9. As proof of concept, we used existing mKate2-encoding sequences inserted in the 5' end of genes as an insertion point for the auxin inducible degron, AID*. This sequence permits reasonably efficient insertion that can be employed using a variety of approaches for different end goals. Our strategy is thus generalizable to many needs.

Marine-Derived Xyloketal Compound Ameliorates MPP+-Induced Neuronal Injury through Regulating of the IRE1/XBP1 Signaling Pathway

The IRE1/XBP1 signaling pathway is the most conserved component of the endoplasmic reticulum unfolded protein response (UPR^ER). Activating this branch to correct defects in ER proteostasis is regarded as a promising anti-Parkinson's disease (PD) strategy. P-53 is a marine-derived xyloketal B analog which exhibited potential neuroprotective activities in previous research studies; however, the molecular mechanism underneath its protective effect remains unknown. Herein, a transcriptomic approach was introduced to explore the protective mechanism of P-53. RNA microarray profiling was conducted based on an MPP⁺-induced C. elegans PD model, and bioinformatics analyses including GO enrichment and PPI network analysis were subsequently performed. In particular, the recovery of the impaired UPR^ER was highlighted as a main physiological change caused by P-53, and a cluster of genes including abu and hsp family genes which are involved in the IRE1/XBP1 branch of the UPR^ER were identified as the key genes related to its neuroprotective effect. The transcription levels of these key genes were validated by RT-qPCR assays. Further results showed that P-53 enhanced the phosphorylation of IRE1, the splicing of xbp-1 mRNA, and the translation of XBP1S and boosted the expression level of the downstream targets of the IRE1/XBP1 signaling pathway. Moreover, it was also demonstrated that P-53 accelerated the scavenging of misfolded α-synuclein and attenuated the correlative mitochondrial dysfunction. Finally, the protective effect of P-53 against MPP⁺-induced dopaminergic neuronal loss was assessed. Taken together, these results revealed that P-53 plays its neuroprotective role through regulating of the IRE1/XBP1 signaling pathway and laid the foundation for its further development as an ER proteostasis-regulating agent.

The role of insulin/IGF-1 signaling in the longevity of model invertebrates, C. elegans and D. melanogaster

Insulin/insulin-like growth factor (IGF)-1 signaling (IIS) pathway regulates aging in many organisms, ranging from simple invertebrates to mammals, including humans. Many seminal discoveries regarding the roles of IIS in aging and longevity have been made by using the roundworm Caenorhabditis elegans and the fruit fly Drosophila melanogaster. In this review, we describe the mechanisms by which various IIS components regulate aging in C. elegans and D. melanogaster. We also cover systemic and tissue-specific effects of the IIS components on the regulation of lifespan. We further discuss IIS-mediated physiological processes other than aging and their effects on human disease models focusing on C. elegans studies. As both C. elegans and D. melanogaster have been essential for key findings regarding the effects of IIS on organismal aging in general, these invertebrate models will continue to serve as workhorses to help our understanding of mammalian aging. [BMB Reports 2016; 49(2): 81-92]

Methodological considerations for heat shock of the nematode Caenorhabditis elegans

Stress response pathways share commonalities across many species, including humans, making heat shock experiments valuable tools for many biologists. The study of stress response in Caenorhabditis elegans has provided great insight into many complex pathways and diseases. Nevertheless, the heat shock/heat stress field does not have consensus as to the timing, temperature, or duration of the exposure and protocols differ extensively between laboratories. The lack of cohesiveness makes it difficult to compare results between groups or to know where to start when preparing your own protocol. We present a discussion of some of the major hurdles to reproducibility in heat shock experiments as well as detailed protocols for heat shock and hormesis experiments.

Transcriptional regulation of gene expression in C. elegans

Protein coding gene sequences are converted to mRNA by the highly regulated process of transcription. The precise temporal and spatial control of transcription for many genes is an essential part of development in metazoans. Thus, understanding the molecular mechanisms underlying transcriptional control is essential to understanding cell fate determination during embryogenesis, post-embryonic development, many environmental interactions, and disease-related processes. Studies of transcriptional regulation in C. elegans exploit its genomic simplicity and physical characteristics to define regulatory events with single-cell and minute-time-scale resolution. When combined with the genetics of the system, C. elegans offers a unique and powerful vantage point from which to study how chromatin-associated proteins and their modifications interact with transcription factors and their binding sites to yield precise control of gene expression through transcriptional regulation.

Revelations from the Nematode Caenorhabditis elegans on the Complex Interplay of Metal Toxicological Mechanisms

Metals have been definitively linked to a number of disease states. Due to the widespread existence of metals in our environment from both natural and anthropogenic sources, understanding the mechanisms of their cellular detoxification is of upmost importance. Organisms have evolved cellular detoxification systems including glutathione, metallothioneins, pumps and transporters, and heat shock proteins to regulate intracellular metal levels. The model organism, Caenorhabditis elegans (C. elegans), contains these systems and provides several advantages for deciphering the mechanisms of metal detoxification. This review provides a brief summary of contemporary literature on the various mechanisms involved in the cellular detoxification of metals, specifically, antimony, arsenic, cadmium, copper, manganese, mercury, and depleted uranium using the C. elegans model system for investigation and analysis.

Evidence for active maintenance of inverted repeat structures identified by a comparative genomic approach

Inverted repeats have been found to occur in both prokaryotic and eukaryotic genomes. Usually they are short and some have important functions in various biological processes. However, long inverted repeats are rare and can cause genome instability. Analyses of C. elegans genome identified long, nearly-perfect inverted repeat sequences involving both divergently and convergently oriented homologous gene pairs and complete intergenic sequences. Comparisons with the orthologous regions from the genomes of C. briggsae and C. remanei show that the inverted repeat structures are often far more conserved than the sequences. This observation implies that there is an active mechanism for maintaining the inverted repeat nature of the sequences.

Temporal regulation of foregut development by HTZ-1/H2A.Z and PHA-4/FoxA

The histone variant H2A.Z is evolutionarily conserved and plays an essential role in mice, Drosophila, and Tetrahymena. The essential function of H2A.Z is unknown, with some studies suggesting a role in transcriptional repression and others in activation. Here we show that Caenorhabditis elegans HTZ-1/H2A.Z and the remodeling complex MYS-1/ESA1–SSL-1/SWR1 synergize with the FoxA transcription factor PHA-4 to coordinate temporal gene expression during foregut development. We observe dramatic genetic interactions between pha-4 and htz-1, mys-1, and ssl-1. A survey of transcription factors reveals that this interaction is specific, and thus pha-4 is acutely sensitive to reductions in these three proteins. Using a nuclear spot assay to visualize HTZ-1 in living embryos as organogenesis proceeds, we show that HTZ-1 is recruited to foregut promoters at the time of transcriptional onset, and this recruitment requires PHA-4. Loss of htz-1 by RNAi is lethal and leads to delayed expression of a subset of foregut genes. Thus, the effects of PHA-4 on temporal regulation can be explained in part by recruitment of HTZ-1 to target promoters. We suggest PHA-4 and HTZ-1 coordinate temporal gene expression by modulating the chromatin environment.

During development, a single fertilized egg gives rise to the different cell types within an embryo. These different cell types are characterized by the different genes that they express. A critical question in biology is how embryonic cells activate genes at the appropriate time and place to generate the different cell types. In this paper, the authors explore temporal regulation of gene expression during formation of an organ, namely the Caenorhabditis elegans foregut. They have discovered that foregut genes require a variant of the canonical H2A histone for the onset of transcription. This variant, called H2A.Z, or htz-1 in C. elegans, promotes transcription by modifying how DNA is packaged within cells. Their data suggest that a key regulator of foregut development, the transcription factor PHA-4, recruits HTZ-1 to pharyngeal promoters, and this association contributes to their timely activation.

Exposure to the metabolic inhibitor sodium azide induces stress protein expression and thermotolerance in the nematode Caenorhabditis elegans

Historically, sodium azide has been used to anesthetize the nematode Caenorhabditis elegans; however, the mechanism by which it survives this exposure is not understood. In this study, we report that exposure of wild-type C elegans to 10 mM sodium azide for up to 90 minutes confers thermotolerance (defined as significantly increased survival probability [SP] at 37 degrees C) on the animal. In addition, sodium dodecyl sulfate-polyacrylamide gel electrophoresis revealed enhanced Hsp70 expression, whereas Western blot analysis revealed the induction of Hsp16. We also tested the only known C elegans Hsp mutant def-21 (codes for Hsp90), which constitutively enters the stress-resistant state known as the dauer larvae. Daf-21 mutants also acquire sodium azide-induced thermotolerance, whereas 3 non-Hsp, constitutive dauer-forming mutants exhibited a variable response to azide exposure. We conclude that the ability of C elegans to survive exposure to azide is associated with the induction of at least 2 stress proteins.

Association of several small heat-shock proteins with reproductive tissues in the nematode Caenorhabditis elegans

Immunohistochemical data on 10 of the 14 small heat-shock (smHSPs) proteins in fourth larval stage and adult Caenorhabditis elegans show that the tissues expressing the greatest number of smHSPs are vulva (HSP12s, HSP43 and, under stress, HSP16s) and spermatheca (HSP12s, HSP25, HSP43 and, under stress, HSP16s). HSP43 is also expressed in male tail structures, and following heat-shock HSP16s are expressed in spermatids and spermatozoa.

Differential expression of individual suppressor tRNA(Trp) gene gene family members in vitro and in vivo in the nematode Caenorhabditis elegans

Eight different amber suppressor tRNA (suptRNA) mutations in the nematode Caenorhabditis elegans have been isolated; all are derived from members of the tRNA(Trp) gene family (K. Kondo, B. Makovec, R. H. Waterston, and J. Hodgkin, J. Mol. Biol. 215:7-19, 1990). Genetic assays of suppressor activity suggested that individual tRNA genes were differentially expressed, probably in a tissue- or developmental stage-specific manner. We have now examined the expression of representative members of this gene family both in vitro, using transcription in embryonic cell extracts, and in vivo, by assaying suppression of an amber-mutated lacZ reporter gene in animals carrying different suptRNA mutations. Individual wild-type tRNA(Trp) genes and their amber-suppressing counterparts appear to be transcribed and processed identically in vitro, suggesting that the behavior of suptRNAs should reflect wild-type tRNA expression. The levels of transcription of different suptRNA genes closely parallel the extent of genetic suppression in vivo. The results suggest that differential expression of tRNA genes is most likely at the transcriptional rather than the posttranscriptional level and that 5' flanking sequences play a role in vitro, and probably in vivo as well. Using suppression of a lacZ(Am) reporter gene as a more direct assay of suptRNA activity in individual cell types, we have again observed differential expression which correlates with genetic and in vitro transcription results. This provides a model system to more extensively study the basis for differential expression of this tRNA gene family.

Baculovirus p35 prevents developmentally programmed cell death and rescues a ced-9 mutant in the nematode Caenorhabditis elegans

Programmed cell death, or apoptosis, occurs throughout the course of normal development in most animals and can also be elicited by a number of stimuli such as growth factor deprivation and viral infection. Certain morphological and biochemical characteristics of programmed cell death are similar among different tissues and species. During development of the nematode Caenorhabditis elegans, a single genetic pathway promotes the death of selected cells in a lineally fixed pattern. This pathway appears to be conserved among animal species. The baculovirus p35-encoding gene (p35) is an inhibitor of virus-induced apoptosis in insect cells. Here we demonstrate that expression of p35 in C. elegans prevents death of cells normally programmed to die. This suppression of developmentally programmed cell death results in appearance of extra surviving cells. Expression of p35 can rescue the embryonic lethality of a mutation in ced-9, an endogenous gene homologous to the mammalian apoptotic suppressor bcl-2, whose absence leads to ectopic cell deaths. These results support the hypothesis that viral infection can activate the same cell death pathway as is used during normal development and suggest that baculovirus p35 may act downstream or independently of ced-9 in this pathway.

Poly(A) tail length of a heat shock protein RNA is increased by severe heat stress, but intron splicing is unaffected

The small heat shock proteins (sHSPs) are induced in all eukaryotes in response to high temperature stress, but are most abundant among members of the plant kingdom where they accumulate in multiple subcellular compartments. We have analyzed the expression of the chloroplast-localized sHSP from Arabidopsis thaliana, HSP21, and characterized the structure of the gene encoding this protein to facilitate future genetic studies on the function of HSP21 in the heat shock response. HSP21 is encoded in Arabidopsis by a single gene whose coding region is interrupted by a single intron. Previous studies have shown that intron processing is disrupted by severe, abrupt heat stress but is protected by pretreatments that induce thermotolerance. The processing of the HSP21 transcript was investigated in response to an abrupt heat stress regime and a gradual heat stress regime, the latter of which is known to confer thermotolerance in plants. Under abrupt stress conditions the HSP21 transcript is somewhat longer than under gradual heat stress conditions. However, the molecular basis for the size difference is not impaired intron splicing, but rather a difference in the length of the poly(A) tail depending on the heat stress regime. The results suggest that an increase in poly(A) tail length may be a generalized response to severe, abrupt heat stress and that poly(A) tail metabolism may be one of numerous cellular processes normally protected in thermotolerant cells from the otherwise damaging effects of high temperature stress.

The ubc-2 gene of Caenorhabditis elegans encodes a ubiquitin-conjugating enzyme involved in selective protein degradation

The ubiquitin-protein conjugation system is involved in a variety of eukaryotic cell functions, including the degradation of abnormal and short-lived proteins, chromatin structure, cell cycle progression, and DNA repair. The ubiquitination of target proteins is catalyzed by a ubiquitin-activating enzyme (E1) and ubiquitin-conjugating enzymes (E2s) and in some cases also requires auxiliary substrate recognition proteins (E3s). Multiple E2s have been found, and these likely possess specificity for different classes of target proteins. Here we report the cloning and characterization of a gene (ubc-2) encoding a ubiquitin-conjugating enzyme which is involved in the selective degradation of abnormal and short-lived proteins in the nematode Caenorhabditis elegans. The nematode ubc-2 gene encodes a 16.7-kDa protein with striking amino acid sequence similarity to Saccharomyces cerevisiae UBC4 and UBC5 and Drosophila UbcD1. When driven by the UBC4 promoter, ubc-2 can functionally substitute for UBC4 in yeast cells; it rescues the slow-growth phenotype of ubc4 ubc5 mutants at normal temperature and restores their ability to grow at elevated temperatures. Western blots (immunoblots) of ubc4 ubc5 yeast cells transformed with ubc-2 reveal a protein of the expected size, which cross-reacts with anti-Drosophila UbcD1 antibody. C. elegans ubc-2 is constitutively expressed at all life cycle stages and, unlike yeast UBC4 and UBC5, is not induced by heat shock. Both trans and cis splicing are involved in the maturation of the ubc-2 transcript. These data suggest that yeast UBC4 and UBC5, Drosophila UbcD1, and C. elegans ubc-2 define a highly conserved gene family which plays fundamental roles in all eukaryotic cells.

The ubc-2 gene of Caenorhabditis elegans encodes a ubiquitin-conjugating enzyme involved in selective protein degradation

The ubiquitin-protein conjugation system is involved in a variety of eukaryotic cell functions, including the degradation of abnormal and short-lived proteins, chromatin structure, cell cycle progression, and DNA repair. The ubiquitination of target proteins is catalyzed by a ubiquitin-activating enzyme (E1) and ubiquitin-conjugating enzymes (E2s) and in some cases also requires auxiliary substrate recognition proteins (E3s). Multiple E2s have been found, and these likely possess specificity for different classes of target proteins. Here we report the cloning and characterization of a gene (ubc-2) encoding a ubiquitin-conjugating enzyme which is involved in the selective degradation of abnormal and short-lived proteins in the nematode Caenorhabditis elegans. The nematode ubc-2 gene encodes a 16.7-kDa protein with striking amino acid sequence similarity to Saccharomyces cerevisiae UBC4 and UBC5 and Drosophila UbcD1. When driven by the UBC4 promoter, ubc-2 can functionally substitute for UBC4 in yeast cells; it rescues the slow-growth phenotype of ubc4 ubc5 mutants at normal temperature and restores their ability to grow at elevated temperatures. Western blots (immunoblots) of ubc4 ubc5 yeast cells transformed with ubc-2 reveal a protein of the expected size, which cross-reacts with anti-Drosophila UbcD1 antibody. C. elegans ubc-2 is constitutively expressed at all life cycle stages and, unlike yeast UBC4 and UBC5, is not induced by heat shock. Both trans and cis splicing are involved in the maturation of the ubc-2 transcript. These data suggest that yeast UBC4 and UBC5, Drosophila UbcD1, and C. elegans ubc-2 define a highly conserved gene family which plays fundamental roles in all eukaryotic cells.

Inverted repeat structure of the Sry locus in mice

The testis-determining gene Sry is located on the short arm of the mouse Y chromosome in a region known to have undergone duplications and rearrangements in comparison with the equivalent portion of the human Y chromosome. Detailed analysis of the Sry genomic locus reveals a further difference in that the mouse Sry open reading frame lies within 2.8 kilobases of unique sequence at the center of a large inverted repeat. This repeat, which is found in both Mus musculus musculus and Mus musculus domesticus Y chromosomes, is not present at the human SRY locus. Recombination involving the repeat region may have led to an 11-kilobase deletion, precisely excising Sry in a line of XY female mice.

Temporal and spatial expression patterns of the small heat shock (hsp16) genes in transgenic Caenorhabditis elegans

The expression of the hsp16 gene family in Caenorhabditis elegans has been examined by introducing hsp16-lacZ fusions into the nematode by transformation. Transcription of the hsp16-lacZ transgenes was totally heat-shock dependent and resulted in the rapid synthesis of detectable levels of beta-galactosidase. Although the two hsp16 gene pairs of C. elegans are highly similar within both their coding and noncoding sequences, quantitative and qualitative differences in the spatial pattern of expression between gene pairs were observed. The hsp16-48 promoter was shown to direct greater expression of beta-galactosidase in muscle and hypodermis, whereas the hsp16-41 promoter was more efficient in intestine and pharyngeal tissue. Transgenes that eliminated one promoter from a gene pair were expressed at reduced levels, particularly in postembryonic stages, suggesting that the heat shock elements in the intergenic region of an hsp16 gene pair may act cooperatively to achieve high levels of expression of both genes. Although the hsp16 gene pairs are never constitutively expressed, their heat inducibility is developmentally restricted; they are not heat inducible during gametogenesis or early embryogenesis. The hsp16 genes represent the first fully inducible system in C. elegans to be characterized in detail at the molecular level, and the promoters of these genes should find wide applicability in studies of tissue- and developmentally regulated genes in this experimental organism.

The spliceosomal snRNAs of Caenorhabditis elegans

Nematodes are the only group of organisms in which both cis- and trans-splicing of nuclear mRNAs are known to occur. Most Caenorhabditis elegans introns are exceptionally short, often only 50 bases long. The consensus donor and acceptor splice site sequences found in other animals are used for both cis- and trans-splicing. In order to identify the machinery required for these splicing events, we have characterized the C. elegans snRNAs. They are similar in sequence and structure to those characterized in other organisms, and several sequence variations discovered in the nematode snRNAs provide support for previously proposed structure models. The C. elegans snRNAs are encoded by gene families. We report here the sequences of many of these genes. We find a highly conserved sequence, the proximal sequence element (PSE), about 65 bp upstream of all 21 snRNA genes thus far sequenced, including the SL RNA genes, which specify the snRNAs that provide the 5' exons in trans-splicing. The sequence of the C. elegans PSE is distinct from PSE's from other organisms.

Information content of Caenorhabditis elegans splice site sequences varies with intron length

A database of sequences of 139 introns from the nematode Caenorhabditis elegans was analyzed using the information measure of Schneider et al. (1986) J. Mol. Biol. 128: 415-431. Statistically significant information is encoded by at least the first 30 nt and last 20 nt of C. elegans introns. Both the quantity and the distribution of information in the 5' splice site sequences differs between the typical short (length less than 75 nt) and rarer long (length greater than 75 nt) introns, with the 5 sites of long introns containing approximately one bit more information. 3' splice site sequences of long and short C. elegans introns differ significantly in the region between -20 and -10 nt.

hsp26 of Saccharomyces cerevisiae is related to the superfamily of small heat shock proteins but is without a demonstrable function

Analysis of the cloned gene confirms that hsp26 of Saccharomyces cerevisiae is a member of the small heat shock protein superfamily. Previous mutational analysis failed to demonstrate any function for the protein. Further experiments presented here demonstrate that hsp26 has no obvious regulatory role and no major effect on thermotolerance. It is possible that the small heat shock protein genes originated as primitive viral or selfish DNA elements.

hsp26 of Saccharomyces cerevisiae is related to the superfamily of small heat shock proteins but is without a demonstrable function

Analysis of the cloned gene confirms that hsp26 of Saccharomyces cerevisiae is a member of the small heat shock protein superfamily. Previous mutational analysis failed to demonstrate any function for the protein. Further experiments presented here demonstrate that hsp26 has no obvious regulatory role and no major effect on thermotolerance. It is possible that the small heat shock protein genes originated as primitive viral or selfish DNA elements.

Sequence and regulation of a gene encoding a human 89-kilodalton heat shock protein

Vertebrate cells synthesize two forms of the 82- to 90-kilodalton heat shock protein that are encoded by distinct gene families. In HeLa cells, both proteins (hsp89 alpha and hsp89 beta) are abundant under normal growth conditions and are synthesized at increased rates in response to heat stress. Only the larger form, hsp89 alpha, is induced by the adenovirus E1A gene product (M. C. Simon, K. Kitchener, H. T. Kao, E. Hickey, L. Weber, R. Voellmy, N. Heintz, and J. R. Nevins, Mol. Cell. Biol. 7:2884-2890, 1987). We have isolated a human hsp89 alpha gene that shows complete sequence identity with heat- and E1A-inducible cDNA used as a hybridization probe. The 5'-flanking region contained overlapping and inverted consensus heat shock control elements that can confer heat-inducible expression on a beta-globin reporter gene. The gene contained 10 intervening sequences. The first intron was located adjacent to the translation start codon, an arrangement also found in the Drosophila hsp82 gene. The spliced mRNA sequence contained a single open reading frame encoding an 84,564-dalton polypeptide showing high homology with the hsp82 to hsp90 proteins of other organisms. The deduced hsp89 alpha protein sequence differed from the human hsp89 beta sequence reported elsewhere (N. F. Rebbe, J. Ware, R. M. Bertina, P. Modrich, and D. W. Stafford (Gene 53:235-245, 1987) in at least 99 out of the 732 amino acids. Transcription of the hsp89 alpha gene was induced by serum during normal cell growth, but expression did not appear to be restricted to a particular stage of the cell cycle. hsp89 alpha mRNA was considerably more stable than the mRNA encoding hsp70, which can account for the higher constitutive rate of hsp89 synthesis in unstressed cells.

Isolation and functional analysis of chicken 90-kDa heat shock protein gene promoter

We report the nucleotide sequence of a 2652 bp derived from a chicken 90-kDa heat shock protein (hsp 90) genomic clone. This fragment contains 890 bp of the 5' flanking region and 1762 bp of structural gene sequence encoding the first 85 amino acids of the protein. The start site of transcription was determined by primer extension and RNase mapping. Two introns have been identified. The first intron presents two features in common with the unique intron of the hsp 83 of drosophila: its location just before the ATG initiation codon and its length of approximately 1.3 Kb. The 5' flanking region contains a TATAA element, a CCAAT box and several putative cis-regulatory elements that might account for the basal level of expression and developmental regulation of the gene. Functional analyses show that hsp 90 gene expression is constitutive and heat inducible and that a full heat shock response requires the cooperativity of two distinct blocks of overlapping heat shock response elements.

Sequence and regulation of a gene encoding a human 89-kilodalton heat shock protein

Vertebrate cells synthesize two forms of the 82- to 90-kilodalton heat shock protein that are encoded by distinct gene families. In HeLa cells, both proteins (hsp89 alpha and hsp89 beta) are abundant under normal growth conditions and are synthesized at increased rates in response to heat stress. Only the larger form, hsp89 alpha, is induced by the adenovirus E1A gene product (M. C. Simon, K. Kitchener, H. T. Kao, E. Hickey, L. Weber, R. Voellmy, N. Heintz, and J. R. Nevins, Mol. Cell. Biol. 7:2884-2890, 1987). We have isolated a human hsp89 alpha gene that shows complete sequence identity with heat- and E1A-inducible cDNA used as a hybridization probe. The 5'-flanking region contained overlapping and inverted consensus heat shock control elements that can confer heat-inducible expression on a beta-globin reporter gene. The gene contained 10 intervening sequences. The first intron was located adjacent to the translation start codon, an arrangement also found in the Drosophila hsp82 gene. The spliced mRNA sequence contained a single open reading frame encoding an 84,564-dalton polypeptide showing high homology with the hsp82 to hsp90 proteins of other organisms. The deduced hsp89 alpha protein sequence differed from the human hsp89 beta sequence reported elsewhere (N. F. Rebbe, J. Ware, R. M. Bertina, P. Modrich, and D. W. Stafford (Gene 53:235-245, 1987) in at least 99 out of the 732 amino acids. Transcription of the hsp89 alpha gene was induced by serum during normal cell growth, but expression did not appear to be restricted to a particular stage of the cell cycle. hsp89 alpha mRNA was considerably more stable than the mRNA encoding hsp70, which can account for the higher constitutive rate of hsp89 synthesis in unstressed cells.

Dynamic changes in the structure and intracellular locale of the mammalian low-molecular-weight heat shock protein

Mammalian cells grown at 37 degrees C contain a single low-molecular-weight heat shock (or stress) protein with an apparent mass of 28 kilodaltons (kDa) whose synthesis increases in cells after exposure to elevated temperatures or other forms of physiologic stress. Herein we present data demonstrating that heat shock protein 28 exists in a number of dynamic states depending upon the physiologic state of the cell. Biochemical fractionation of 37 degrees C cells in the absence of nonionic detergent revealed that the 28-kDa protein partitioned approximately equally between the soluble and insoluble fractions. The addition of detergent in the fractionation procedure resulted in all of the protein distributed within the soluble phase. In contrast, in cells first heat shocked and then fractionated in the presence of detergent, most of the 28-kDa protein was found within the insoluble fraction. These biochemical results appeared entirely consistent with indirect immunofluorescence experiments, demonstrating that the 28-kDa protein resided within the perinuclear region of 37 degrees C cells in close proximity to the Golgi complex. After heat shock treatment, the 28-kDa protein relocalized within the nucleus and resisted detergent extraction. The extent of 28-kDa protein redistribution into the nucleus and its detergent insolubility increased as a function of the severity of the heat shock treatment. With time of recovery from the heat treatment there occurred a gradual return of the 28-kDa protein into the detergent-soluble phase. Concomitant with these changes in 28-kDa protein solubility was a corresponding change in the apparent size of the protein as determined by gel filtration. While at 37 degrees C cells the protein exhibited a mass of 200 to 800 kDa; after heat shock the protein assumed sizes of 2 MDa or greater. Using immunoelectron microscopy, we show an accumulation of these aggregates of 28-kDa protein within the nucleus. Finally, we show that the heat-dependent redistribution of the 28-kDa protein from the cytoplasm into the nucleus was greatly diminished when the cells were first rendered thermotolerant, and we suggest that this simple assay (i.e., 28-kDa protein detergent solubility) may prove useful in evaluating the thermotolerant status of a cell or tissue.

UbiA, the major polyubiquitin locus in Caenorhabditis elegans, has unusual structural features and is constitutively expressed

Ubiquitin is a multifunctional 76-amino-acid protein which plays critical roles in many aspects of cellular metabolism. In Caenorhabditis elegans, the major source of ubiquitin RNA is the polyubiquitin locus, UbiA. UbiA is transcribed as a polycistronic mRNA which contains 11 tandem repeats of ubiquitin sequence and possesses a 2-amino-acid carboxy-terminal extension on the final repeat. The UbiA locus possesses several unusual features not seen in the ubiquitin genes of other organisms studied to date. Mature UbiA mRNA acquires a 22-nucleotide leader sequence via a trans-splicing reaction involving a 100-nucleotide splice leader RNA derived from a different chromosome. UbiA is also unique among known polyubiquitin genes in containing four cis-spliced introns within its coding sequence. Thus, UbiA is one of a small class of genes found in higher eucaryotes whose heterogeneous nuclear RNA undergoes both cis and trans splicing. The putative promoter region of UbiA contains a number of potential regulatory elements: (i) a cytosine-rich block, (ii) two sequences resembling the heat shock regulatory element, and (iii) a palindromic sequence with homology to the DNA-binding site of the mammalian steroid hormone receptor. The expression of the UbiA gene has been studied under various heat shock conditions and has been monitored during larval moulting and throughout the major stages of development. These studies indicate that the expression of the UbiA gene is not inducible by acute or chronic heat shock and does not appear to be under nutritional or developmental regulation in C. elegans.

Key features of heat shock regulatory elements

The promoters of heat shock protein genes are among the best-studied inducible eucaryotic promoters. Regions responsible for heat regulation have been identified previously by deletion experiments with several different heat shock genes. In this paper the critical importance of two novel features of heat shock regulatory elements was investigated. First, the elements were modular and, as a consequence, displayed a characteristic 5-nucleotide periodicity produced by multiple GAA blocks that were arranged in alternating orientations and at 2-nucleotide intervals. Functional heat shock regulatory elements appeared to include three or more of these blocks. Second, the nucleotides at the two positions immediately upstream from GAA segments played an important role in defining the competence of regulatory elements.

Evidence for a class of very small introns in the gene for hypoxanthine-guanine phosphoribosyltransferase in Schistosoma mansoni

The single copy gene for the hypoxanthine-guanine phosphoribosyltransferase (HGPRTase) of the parasitic trematode, Schistosoma mansoni, contains seven introns, the first four of which are only 31, 33, 42, and 32 bases in length. These are the smallest introns ever discovered in a non-viral nuclear gene coding for protein. These very small introns possess the canonical GT...AG splice site sequences but lack the branching sequence, the secondary structure, and the minimum size of approximately 50 bases believed to be required for the splicing of eucaryotic mRNA precursors. Evidently, a somewhat different splicing mechanism for the transcripts of these very small introns is necessary. Their discovery within the genes of helminths raises theoretical considerations for the evolution of introns in eucaryotes.

The intracellular location of yeast heat-shock protein 26 varies with metabolism

An antibody highly specific for heat-shock protein (hsp)26, the unique small hsp of yeast, and mutants carrying a deletion of the HSP26 gene were used to examine the physical properties of the protein and to determine its intracellular distribution. The protein was found in complexes with a molecular mass of greater than 500 kD. Thus, it has all of the characteristics, including sequence homology and induction patterns, of small hsps from other organisms. When log-phase cells growing in glucose were heat shocked, hsp26 concentrated in nuclei and continued to concentrate in nuclei when these cells were returned to normal temperatures for recovery. However, hsp26 did not concentrate in nuclei under a variety of other conditions. For example, in early stationary-phase cells hsp26 is induced at normal growth temperatures. This protein was generally distributed throughout the cells, even after heat shock. Similarly, in cells genetically engineered to synthesize hsp26 in the presence of galactose, hsp26 did not concentrate in nuclei, with or without a heat shock. To determine if the failure of hsp26 to concentrate in the nucleus of these cells was due to the fact that the protein had been produced at 25 degrees C or to a difference in the physiological state of the cell, we investigated the distribution of the heat-induced protein in cells grown under several different conditions. In wild-type cells grown in galactose or acetate and in mitochondrial mutants grown in glucose or galactose, hsp26 also failed to concentrate in nuclei with a heat shock. We conclude that the intracellular location of hsp26 in yeast depends upon the physiological state of the cell and not simply upon the presence or absence of heat stress. Our findings may explain why previous investigations of the intracellular localization of small hsps in a variety of organisms have yielded seemingly contradictory results.

UbiA, the major polyubiquitin locus in Caenorhabditis elegans, has unusual structural features and is constitutively expressed

Ubiquitin is a multifunctional 76-amino-acid protein which plays critical roles in many aspects of cellular metabolism. In Caenorhabditis elegans, the major source of ubiquitin RNA is the polyubiquitin locus, UbiA. UbiA is transcribed as a polycistronic mRNA which contains 11 tandem repeats of ubiquitin sequence and possesses a 2-amino-acid carboxy-terminal extension on the final repeat. The UbiA locus possesses several unusual features not seen in the ubiquitin genes of other organisms studied to date. Mature UbiA mRNA acquires a 22-nucleotide leader sequence via a trans-splicing reaction involving a 100-nucleotide splice leader RNA derived from a different chromosome. UbiA is also unique among known polyubiquitin genes in containing four cis-spliced introns within its coding sequence. Thus, UbiA is one of a small class of genes found in higher eucaryotes whose heterogeneous nuclear RNA undergoes both cis and trans splicing. The putative promoter region of UbiA contains a number of potential regulatory elements: (i) a cytosine-rich block, (ii) two sequences resembling the heat shock regulatory element, and (iii) a palindromic sequence with homology to the DNA-binding site of the mammalian steroid hormone receptor. The expression of the UbiA gene has been studied under various heat shock conditions and has been monitored during larval moulting and throughout the major stages of development. These studies indicate that the expression of the UbiA gene is not inducible by acute or chronic heat shock and does not appear to be under nutritional or developmental regulation in C. elegans.

Dynamic changes in the structure and intracellular locale of the mammalian low-molecular-weight heat shock protein

Mammalian cells grown at 37 degrees C contain a single low-molecular-weight heat shock (or stress) protein with an apparent mass of 28 kilodaltons (kDa) whose synthesis increases in cells after exposure to elevated temperatures or other forms of physiologic stress. Herein we present data demonstrating that heat shock protein 28 exists in a number of dynamic states depending upon the physiologic state of the cell. Biochemical fractionation of 37 degrees C cells in the absence of nonionic detergent revealed that the 28-kDa protein partitioned approximately equally between the soluble and insoluble fractions. The addition of detergent in the fractionation procedure resulted in all of the protein distributed within the soluble phase. In contrast, in cells first heat shocked and then fractionated in the presence of detergent, most of the 28-kDa protein was found within the insoluble fraction. These biochemical results appeared entirely consistent with indirect immunofluorescence experiments, demonstrating that the 28-kDa protein resided within the perinuclear region of 37 degrees C cells in close proximity to the Golgi complex. After heat shock treatment, the 28-kDa protein relocalized within the nucleus and resisted detergent extraction. The extent of 28-kDa protein redistribution into the nucleus and its detergent insolubility increased as a function of the severity of the heat shock treatment. With time of recovery from the heat treatment there occurred a gradual return of the 28-kDa protein into the detergent-soluble phase. Concomitant with these changes in 28-kDa protein solubility was a corresponding change in the apparent size of the protein as determined by gel filtration. While at 37 degrees C cells the protein exhibited a mass of 200 to 800 kDa; after heat shock the protein assumed sizes of 2 MDa or greater. Using immunoelectron microscopy, we show an accumulation of these aggregates of 28-kDa protein within the nucleus. Finally, we show that the heat-dependent redistribution of the 28-kDa protein from the cytoplasm into the nucleus was greatly diminished when the cells were first rendered thermotolerant, and we suggest that this simple assay (i.e., 28-kDa protein detergent solubility) may prove useful in evaluating the thermotolerant status of a cell or tissue.

Key features of heat shock regulatory elements

The promoters of heat shock protein genes are among the best-studied inducible eucaryotic promoters. Regions responsible for heat regulation have been identified previously by deletion experiments with several different heat shock genes. In this paper the critical importance of two novel features of heat shock regulatory elements was investigated. First, the elements were modular and, as a consequence, displayed a characteristic 5-nucleotide periodicity produced by multiple GAA blocks that were arranged in alternating orientations and at 2-nucleotide intervals. Functional heat shock regulatory elements appeared to include three or more of these blocks. Second, the nucleotides at the two positions immediately upstream from GAA segments played an important role in defining the competence of regulatory elements.

Structure and evolution of a family of interspersed repetitive DNA sequences in Caenorhabditis elegans

The structure of three members of a repetitive DNA family from the genome of the nematode Caenorhabditis elegans has been studied. The three repetitive elements have a similar unitary structure consisting of two 451-bp sequences in inverted orientation separated by 491 bp, 1.5 kb, and 2.5 kb, respectively. The 491-bp sequence separating the inverted 451-bp sequences of the shortest element is found adjacent to one of the repeats in the other two elements as well. The combination of the three sequences we define as the basic repetitive unit. Comparison of the nucleotide sequences of the three elements has allowed the identification of the one most closely resembling the primordial repetitive element. Additionally, a process of co-evolution is evident that results in the introduction of identical sequence changes into both copies of the inverted sequence within a single unit. Possible mechanisms are discussed for the homogenization of these sequences. A direct test of one possible homogenization mechanism, namely homologous recombination between the inverted sequences accompanied by gene conversion, shows that recombination between the inverted repeats does not occur at high frequency.

Expression of intron-containing C. elegans heat shock genes in mouse cells demonstrates divergence of 3' splice site recognition sequences between nematodes and vertebrates, and an inhibitory effect of heat shock on the mammalian splicing apparatus

Splicing of a pair of intron-containing heat shock genes from Caenorhabditis elegans has been studied in transfected mouse cells. The hsp16-1 and hsp16-48 genes of C. elegans encode 16,000 Da heat shock polypeptides. Each gene contains a short intron of 52 (hsp16-1) or 55 (hsp16-48) base pairs. When these genes were introduced into mouse cells, they were efficiently induced following heat shock, but splicing of the introns was abnormal. In mouse cells, cleavage of the hsp16 transcripts occurred at the correct 5' splice sites, but the 3' splice sites were located at AG dinucleotides downstream of the correct sites. This aberrant splicing was not solely due to the small size of the C. elegans introns, since a hsp16-1 gene containing an intron enlarged by tandem duplication showed exactly the same splicing pattern. The mouse cells thus seem to be unable to recognize the natural 3' splice sites of the C. elegans transcripts. The efficiency of splicing was greatly reduced under heat shock conditions, and unspliced transcripts accumulated in the nucleus. During a subsequent recovery period at 37 degrees C, these transcripts were spliced and transported to the cytoplasm.

A germline transformation analysis reveals flexibility in the organization of heat shock consensus elements

Maximal expression of the Drosophila heat shock gene hsp70 can be activated by a pair of heat shock consensus elements (HSE's) positioned close to the transcription start site. In contrast, required HSE's of other heat shock genes (i.e., hsp26, 27, 23) are located several hundred base pairs (bp) farther upstream of their start sites. Using germline transformation, we analyzed the requirements for HSE organization in the hsp70 and hsp26 regulatory regions. A 51 bp fragment containing the two proximal hsp70 HSE's was sufficient to rescue the heat shock response of an hsp26-lacZ gene devoid of its HSE's. Heat inducibility was restored with either orientation of the fragment relative to the hsp26 transcription start. In hsp70 gene constructions, relocation of hsp70 HSE's to more remote positions by inserting 127 or 331 bp into the regulatory region failed to substantially reduce expression. Thus, in contrast to their native configurations, the hsp26 promoter can be activated by HSE's solely in a proximal position and the hsp70 promoter can be activated by remote HSE's. In addition, a simple and sensitive assay for quantitative measurement of beta-galactosidase activity in crude fly extracts is described.

Efficient transcription of a Caenorhabditis elegans heat shock gene pair in mouse fibroblasts is dependent on multiple promoter elements which can function bidirectionally

A divergently transcribed pair of Caenorhabditis elegans hsp16 genes was introduced into mouse fibroblasts by stable transfection with vectors containing bovine papillomavirus plasmid maintenance sequences and a selectable gene. The hsp16 genes were transcriptionally inactive in the mouse cells under normal growth conditions and were strongly induced by heat shock or arsenite. In a cell line with 12 copies of the gene pair, there were estimated to be more than 10,000 hsp16 transcripts in each cell after 2 h of heat shock treatment. The hsp16 transcript levels were more than 100 times higher than those of a gene with a herpes simplex virus thymidine kinase gene promoter carried on the same vector. A single heat shock promoter element (HSE) could activate bidirectional transcription of the two hsp16 genes when placed between the two TATA elements, but the transcriptional efficiency was reduced 10-fold relative to that of the wild-type gene pair. Four overlapping HSEs positioned between the two TATA elements resulted in inducible bidirectional transcription at greater than wild-type levels. The number of HSEs can therefore be a major determinant of the promoter strength of heat-inducible genes in mammalian cells. Partial disruption of an alternating purine-pyrimidine sequence between the two hsp16 genes had no significant effect on their transcriptional activity.

Efficient transcription of a Caenorhabditis elegans heat shock gene pair in mouse fibroblasts is dependent on multiple promoter elements which can function bidirectionally

A divergently transcribed pair of Caenorhabditis elegans hsp16 genes was introduced into mouse fibroblasts by stable transfection with vectors containing bovine papillomavirus plasmid maintenance sequences and a selectable gene. The hsp16 genes were transcriptionally inactive in the mouse cells under normal growth conditions and were strongly induced by heat shock or arsenite. In a cell line with 12 copies of the gene pair, there were estimated to be more than 10,000 hsp16 transcripts in each cell after 2 h of heat shock treatment. The hsp16 transcript levels were more than 100 times higher than those of a gene with a herpes simplex virus thymidine kinase gene promoter carried on the same vector. A single heat shock promoter element (HSE) could activate bidirectional transcription of the two hsp16 genes when placed between the two TATA elements, but the transcriptional efficiency was reduced 10-fold relative to that of the wild-type gene pair. Four overlapping HSEs positioned between the two TATA elements resulted in inducible bidirectional transcription at greater than wild-type levels. The number of HSEs can therefore be a major determinant of the promoter strength of heat-inducible genes in mammalian cells. Partial disruption of an alternating purine-pyrimidine sequence between the two hsp16 genes had no significant effect on their transcriptional activity.

Complete cDNA sequence of human preceruloplasmin

A cDNA for human ceruloplasmin (EC 1.16.3.1) was identified in a human liver cDNA library by screening with two mixtures of synthetic oligodeoxyribonucleotides that were complementary to two regions of ceruloplasmin mRNA as predicted from the amino acid sequence of plasma ceruloplasmin. The resulting clone (phCP1) contained DNA coding for amino acid residues 202-1046 of the protein, followed by a stop codon, a 3' untranslated region of 123 base pairs, and a poly(A) tail. To isolate cDNAs encoding the 5' end of ceruloplasmin mRNA, a cDNA library was constructed in lambda gt10. The cDNA for this library was synthesized by reverse transcription of human liver poly(A)+ RNA, using random oligonucleotides as primers. When this cDNA library was screened by using a 5' fragment of phCP1 as a hybridization probe, several positive clones were identified. One of these clones (lambda hCP1) contained DNA coding for a probable signal peptide of 19 amino acid residues followed by DNA coding for residues 1-380 of plasma ceruloplasmin. Blot hybridization analysis showed that ceruloplasmin mRNA from human liver and the human hepatoma cell line HepG2 is 3700 nucleotides in size. Liver contained an additional mRNA species that is like ceruloplasmin mRNA and is 4500 nucleotides in size. Comparison of the complete nucleotide sequences of human ceruloplasmin cDNA and human clotting factor VIII cDNA showed regions of sequence homology, suggesting that these two proteins have evolved from a common ancestor.

Sequence and organization of genes encoding the human 27 kDa heat shock protein

The 27 kDa human heat shock protein (hsp27) is encoded by a gene family of 4 members. Two genomic fragments hybridizing to cDNA encoding hsp27 have been isolated, characterized, and sequenced. One clone is a member of a cluster of three genes linked within a 14-18 kb region of the genome and encodes a transcript interrupted by two intervening sequences. A single open reading frame encodes a polypeptide of 22,300 deduced molecular weight. The 5' flanking region contains two transcription start sites and sequences homologous to the Drosophila consensus heat inducible control element. Induction of both potential transcripts follows heat shock in vivo. Accurate heat inducible transcription occurs at both start sites after injection into Xenopus oocytes. The second genomic clone is a processed pseudogene lacking promoter elements and is unlinked with the other members of the hsp27 gene family. The amino acid sequence of human hsp27 shows striking homology with mammalian alpha crystallin, and contains a region towards the carboxy terminus which shares homology with the small hsp of Drosophila and other organisms.

Heat shock locus 93D of Drosophila melanogaster: a spliced RNA most strongly conserved in the intron sequence

The Drosophila melanogaster heat shock locus at 93D encodes at least three overlapping transcripts, 10-12 kilobases (kb), 1.9 kb, and 1.2 kb. The abundance of the three transcripts is significantly increased during heat shock; however, all are also found in non-heat-shocked cells. The 1.2-kb transcript is found in the cytoplasm. Sequence analysis of a 1.1-kb cDNA clone representing sequences within the 1.2-kb transcript and comparison to genomic sequences indicate that it is spliced; 700 base pairs of sequence found in genomic DNA are removed from the middle of the transcript. Sequence analysis further suggests that this RNA does not encode a heat shock protein. The largest open reading frame beginning with a methionine codon would encode a polypeptide of 34 amino acids. We have not been able to detect a heat shock-induced polypeptide of this size. A DNA clone from the analogous heat shock puff of Drosophila hydei has been analyzed by hybridization with the small subclones used to sequence the D. melanogaster cDNA plus a genomic fragment containing the 700-base-pair intron. Results of this hybridization indicated strong homology of the intron fragment. Weaker homology was detected with the two small fragments flanking the intron. Other fragments of the D. melanogaster cDNA showed no hybridization to the cloned D. hydei puff DNA.