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

Thermal Control of Engineered T-cells

Genetically engineered T-cells are being developed to perform a variety of therapeutic functions. However, no robust mechanisms exist to externally control the activity of T-cells at specific locations within the body. Such spatiotemporal control could help mitigate potential off-target toxicity due to incomplete molecular specificity in applications such as T-cell immunotherapy against solid tumors. Temperature is a versatile external control signal that can be delivered to target tissues in vivo using techniques such as focused ultrasound and magnetic hyperthermia. Here, we test the ability of heat shock promoters to mediate thermal actuation of genetic circuits in primary human T-cells in the well-tolerated temperature range of 37-42 °C, and introduce genetic architectures enabling the tuning of the amplitude and duration of thermal activation. We demonstrate the use of these circuits to control the expression of chimeric antigen receptors and cytokines, and the killing of target tumor cells. This technology provides a critical tool to direct the activity of T-cells after they are deployed inside the body.

High fat diet induces microbiota-dependent silencing of enteroendocrine cells

Enteroendocrine cells (EECs) are specialized sensory cells in the intestinal epithelium that sense and transduce nutrient information. Consumption of dietary fat contributes to metabolic disorders, but EEC adaptations to high fat feeding were unknown. Here, we established a new experimental system to directly investigate EEC activity in vivo using a zebrafish reporter of EEC calcium signaling. Our results reveal that high fat feeding alters EEC morphology and converts them into a nutrient insensitive state that is coupled to endoplasmic reticulum (ER) stress. We called this novel adaptation 'EEC silencing'. Gnotobiotic studies revealed that germ-free zebrafish are resistant to high fat diet induced EEC silencing. High fat feeding altered gut microbiota composition including enrichment of Acinetobacter bacteria, and we identified an Acinetobacter strain sufficient to induce EEC silencing. These results establish a new mechanism by which dietary fat and gut microbiota modulate EEC nutrient sensing and signaling.

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]

Artificial mammalian gene regulation networks-novel approaches for gene therapy and bioengineering

Recently developed strategies for targeted molecular interventions in mammalian cells have created novel opportunities in biotechnological and biomedical research with huge economic and therapeutic impact: the design of mammalian cells with desired phenotypes for biopharmaceutical manufacturing, tissue engineering and gene therapy. These advances have been enabled by constructing artificial gene regulation systems with control modalities similar to those evolved in key regulatory networks of mammalian cells. This review highlights recurring cellular regulation strategies and artificial gene regulation technology currently in use for rational reprogramming of cellular key events including metabolism, growth, differentiation and cell death to achieve sophisticated bioprocess and therapeutic goals.

Structure and promoter activity of the 5' flanking region of ace-1, the gene encoding acetylcholinesterase of class A in Caenorhabditis elegans

We report the structure and the functional activity of the promoter region of ace-1, the gene encoding acetylcholinesterase of class A in the nematode Caenorhabditis elegans. We found that ace-1 was trans -spliced to the SL1 spliced leader and that transcription was initiated at a cluster of multiple starts. There was neither a TATA nor a CAAT box at consensus distances from these starts. Interspecies sequence comparison of the 5' regions of ace-1 in C. elegans and in the related nematode Caenorhabditis briggsae identified four blocks of conserved sequences located within a sequence of 2.4 kilobases upstream from the initiator ATG. In vitro expression of CAT reporter genes in mammalian cells allowed the determination of a minimal promoter in the first 288 nucleotides. In phenotype rescue experiments in vivo, the ace-1 gene containing 2.4 kilobases of 5' flanking region of either C. elegans or C. briggsae was found to restore a coordinated mobility to the uncoordinated double mutants ace-1(-);ace-2(-)of C. elegans. This showed that the ace-1 promoter was contained in 2.4 kilobases of the 5' region, and indicated that cis -regulatory elements as well as coding sequences of ace-1 were functionally conserved between the two nematode species. The pattern of ace-1 expression was established through microinjection of Green Fluorescent Protein reporter gene constructs and showed a major mesodermal expression. Deletion analysis showed that two of the four blocks of conserved sequences act as tissue-specific activators. The distal block is a mesodermal enhancer responsible for the expression in body wall muscle cells, anal sphincter and vulval muscle cells. Another block of conserved sequence directs expression in pharyngeal muscle cells pm5 and three pairs of cephalic sensory neurons.

Inducible gene expression in the nervous system of transgenic mice

Gene function during mammalian development is often studied by making irreversible changes to the genome. This approach has a major drawback in that the function of the gene in question must be deduced from the phenotype of animals that have been deficient for the product of the disrupted gene throughout ontogeny. Compensation for the loss of the gene product could yield an apparently unaltered phenotype. Alternatively, the changes in the regulation of other genes could yield a misleading phenotype. If the genetic manipulation results in embryonic or neonatal lethality, gene function at later stages of development cannot be analyzed. It would thus be highly advantageous if the expression of a particular gene could be restricted both temporally and spatially through the use of an inducible genetic system. This paper describes the various inducible genetic expression systems developed for use in mammalian cells, with particular emphasis on their application in the nervous system of transgenic mice.

Molecular mechanisms regulating TNF-alpha production by tumor-associated macrophages

The molecular mechanisms that regulate the production and/or functional activity of intratumoral tumor necrosis factor-alpha (TNF-alpha) remain poorly defined. To begin to address this issue we have examined the level of TNF-alpha mRNA and protein produced by macrophages present within immunogenic Fsa-R and non-immunogenic Fsa-N tumors grown in syngeneic Lps(d) C3H/HeJ and Lps(n) C3H/HeN mice. The results obtained indicate that macrophages isolated from tumors grown in Lps(d) C3H/HeJ mice express 5-10-fold less TNF-alpha than equivalent cells present in tumors grown in Lps(n) C3H/HeN mice. These data suggest that the mechanisms that operate within the tumor microenvironment to induce the production of TNF-alpha act, at least in part, via the same signal transduction pathway that is defective in Lps(d) C3H/HeJ mice. Interestingly, despite such differences in TNF-alpha production, tumors inoculated into C3H/HeJ and C3H/HeN mice grew at a similar rate and contained an almost identical proportion of macrophages. Moreover, tumor cells purified from tumors grown in C3H/HeJ and C3H/HeN mice produced similar quantities of the TNF-alpha-inducible cytokine GM-CSF. Thus, although differences in the level of TNF-alpha produced within tumors grown in C3H/HeN and C3H/HeJ mice are readily demonstrable, such differences appear to have little direct impact on the outcome of tumor growth.

Inhibitory effect of locally produced and exogenous interleukin-6 on tumor growth in vivo

In order to define the potential antitumor activity of the multifunctional cytokine interleukin-6 (IL-6), retrovirus-mediated gene transfer was used to introduce and express a cDNA encoding human IL-6 in the murine fibrosarcoma cell line Fsa-R. Although these genetically modified tumor cells appeared morphologically and phenotypically identical to control Fsa-R cells and had a similar plating efficiency in vitro, they were found to exhibit greatly reduced tumorigenicity in vivo following intravenous injection into syngeneic recipients. Exogenous IL-6 was shown to produce a similar inhibition of tumor growth in the lung if administered intraperitoneally. In contrast, tumor growth in subcutaneous sites was inhibited only if the tumor cells were engineered to express IL-6 locally, or if IL-6 was administered intratumorally. Intraperitoneal injection of IL-6 had no inhibitory effect. Tumors that did grow from IL-6-producing tumor cell inocula in subcutaneous sites were found to contain large numbers of macrophages. These results demonstrate that the antitumor activity of systemically administered IL-6 varies depending on the site of tumor growth and suggest an important role for IL-6 in the recruitment, proliferation and/or survival of tumor-associated macrophages.

Sequence requirements for myosin gene expression and regulation in Caenorhabditis elegans

Four Caenorhabditis elegans genes encode muscle-type specific myosin heavy chain isoforms: myo-1 and myo-2 are expressed in the pharyngeal muscles; unc-54 and myo-3 are expressed in body wall muscles. We have used transformation-rescue and lacZ fusion assays to determine sequence requirements for regulated myosin gene expression during development. Multiple tissue-specific activation elements are present for all four genes. For each of the four genes, sequences upstream of the coding region are tissue-specific promoters, as shown by their ability to drive expression of a reporter gene (lacZ) in the appropriate muscle type. Each gene contains at least one additional tissue-specific regulatory element, as defined by the ability to enhance expression of a heterologous promoter in the appropriate muscle type. In rescue experiments with unc-54, two further requirements apparently independent of tissue specificity were found: sequences within the 3' non-coding region are essential for activity while an intron near the 5' end augments expression levels. The general intron stimulation is apparently independent of intron sequence, indicating a mechanistic effect of splicing. To further characterize the myosin gene promoters and to examine the types of enhancer sequences in the genome, we have initiated a screen of C. elegans genomic DNA for fragments capable of enhancing the myo-2 promoter. The properties of enhancers recovered from this screen suggest that the promoter is limited to muscle cells in its ability to respond to enhancers.

The Hsp70 heat-shock gene family of the mosquito Anopheles albimanus

Four Hsp70 genes of the malaria vector Anopheles albimanus were isolated from a genomic DNA library as two non-overlapping clones each containing a pair of divergently transcribed genes having 75% DNA sequence similarity to the protein-coding regions of the Drosophila melanogaster Hsp70 genes. The clones were assigned to two loci on chromosome 2R by in situ hybridization. These clones hybridize strongly to heat-shock but only weakly to non-shocked mosquito RNA. The Hsp70 gene family of A. albimanus is undergoing concerted evolution probably by gene conversion. The general arrangement of the genes suggests that divergently transcribed pairs of genes at two loci is an ancient Dipteran arrangement predating the Nematocera/Cyclorrapha divergence.

Mutational analysis of a plant heat shock element

A total of 32 mutations were generated within the TATA-proximal site 1 (-72 to -47) of soybean heat shock gene Gmhsp17.5E in order to functionally define the optimal configuration of sequences within the heat shock element (HSE). Mutants were tested in vivo utilizing sunflower tumors transformed by a T-DNA based vector. Promoter activity was determined by S1 nuclease hybrid protection analysis of tumor transcripts. A total of five repeats (5'-nGAAn-3' or 5'-nTTCn-3') which comprise the HSE at site 1 were required for full transcription induction by heat stress. Analysis of non-conserved bases flanking the central trinucleotide block indicated that 5'-aGAAg'-3' is the optimum sequence for the 5 bp repeat.

The complex CD44 transcriptional unit; alternative splicing of three internal exons generates the epithelial form of CD44

We have utilized the polymerase chain reaction (PCR) to isolate a 3.5 kilobase pair (kb) genomic fragment that encodes the additional extracellular domain unique to the epithelial isoform of CD44 (CD44E). Nucleotide sequence was determined for this complete region and sequence comparison to our previously determined CD44R1 and CD44R2 cDNA sequences revealed the R region to be comprised of three exons of 102 bp, 90 bp, and 204 bp. Northern blot analysis of CD44 expressing cell lines confirmed the presence of CD44R1 transcripts and indicates that the epithelial domain may be inserted through alternative splicing into all CD44 transcript classes. Southern blot analysis of the CD44E genomic fragments is consistent with a single copy per human haploid genome. The data presented here further supports our model of the human CD44 transcriptional unit as a single gene complex that utilizes an invariant 5' initiation site, alternative internal and 3' end splicing, and multiple poly (A) sites to generate through RNA processing a diverse number of human CD44 isoforms.

In Vitro Interaction of Nuclear Proteins with the Promoter of Soybean Heat Shock Gene Gmhsp17.5E

Proteins present in crude nuclear extracts of soybean (Glycine max) plumules were shown to bind in vitro to the 5' flanking sequences of the soybean heat shock gene Gmhsp17.5E. The specificity of binding activity present in extracts from both control (28 degrees C) and heat shocked (40 degrees C) tissues was demonstrated by reciprocal competition experiments using gel mobility retardation assays. Footprinting experiments using DNase I with crude nuclear extracts indicated that a continuous stretch of 5' flanking sequences extending from -40 to -153 was protected from digestion in vitro. Nuclear proteins that were partially purified by heparin agarose chromatography were shown to bind specific TATA-proximal sequences containing the heat shock consensus elements (HSEs) (-73 to -49; -107 to -84) and AT-rich motifs (-119 to -153). Other binding sites within AT-rich sequences (-906 to -888, -868 to 863, -859 to 853, and -841 to -830), distal HSE elements (-568 to -532) and a TATA/dyad (-234 to -207) were also identified by DNase I footprinting of TATA-distal probes. DNA binding activities specific for the HSE and AT-rich sequences were present in nuclear extracts from both control and heat shocked tissues. Both types of binding activity were increased after heat shock treatment; HSE binding increased from 1.8- to 2.7-fold, and binding to AT-rich sequences showed an increase from 1.3- to 1.7-fold.

The differentially expressed 16-kD heat shock genes of Caenorhabditis elegans exhibit differential changes in chromatin structure during heat shock

The 16-kD heat shock genes of Caenorhabditis elegans are encoded by four highly similar genes, arranged as divergently transcribed pairs. In spite of the high level of identity that exists between the HSP16 genes, after 2 hr of heat shock the mRNA from one locus accumulates at 7-14 times the level of that from the other locus. To determine if differential HSP16 gene transcriptional activity contributes to these differences, we examined the chromatin structure of the HSP16 genes in nonshocked embryos and in embryos undergoing both the initial phases of heat shock and after 2 hr of heat shock. To carry out these studies, we developed a nuclei isolation procedure that has allowed us to prepare large amounts of nuclei from C. elegans embryos, larvae, and adults that are essentially free of endogenous nuclease and protease activities and appear to be an excellent substrate for investigating chromatin structure in C. elegans. This procedure has enabled us to report the first observations of C. elegans basic chromatin structure, as well as characterize HSP16 chromatin structure in detail. The data suggest that differential HSP16 RNA accumulation following 2 hr of heat shock appears to be correlated with a change in the chromatin structure of one of the HSP16 loci to a preinduction, transcriptionally inactive configuration.

Differential regulation of closely related members of the hsp16 gene family in Caenorhabditis elegans

The heat-inducible genes encoding 16-kD heat shock polypeptides in Caenorhabditis elegans are found at two separate loci, one containing the 16-1 and 16-48 genes (locus A), and the other, the 16-2 and 16-41 genes (locus B). Despite the highly conserved structures of these genes and their promoters, the B locus produces up to sevenfold more mRNA during heat induction than does the A locus. Since there are two copies of the 16-1 and 16-48 genes at the A locus, the discrepancy in mRNA production is actually as high as 14:1 on a per gene basis. Measurements of the rate of hsp16 mRNA decay during recovery from a heat shock suggest that this difference is not caused by differential mRNA stability; furthermore, nuclear runon experiments yield rates of transcription for the 16-1/48 locus that are approximately threefold higher than those from the 16-2/41 locus. The higher levels of mRNA from the 16-2/41 locus, particularly at longer induction times, seem to be due to a marked difference in the temporal pattern of mRNA production from the two loci. While both loci are transiently activated by a heat shock, the 16-1 and 16-48 genes of the A locus are down-regulated to a lower transcription rate sooner than the genes from the B locus.

Sequence analysis of the complete Caenorhabditis elegans myosin heavy chain gene family

The sequences of three myosin heavy chain (MHC) genes from Caenorhabditis elegans, myo-1, 2 and 3, are presented. These genes, together with unc-54, comprise the entire nematode sacromeric MHC family. Comparison of nematode MHC sequences and sarcomeric, smooth and non-muscle MHCs from other organisms highlights conserved sequence features of the MHC rod believed to be important for thick filament assembly. These include: conservation of sequence differences between individual 28 amino acid repeats; invariant placements of large aromatic residues, such as tryptophan, in the rod sequences; conservation of "weak spots" in the hydrophobic seam; and conservation of non-uniform charge distributions along the length of the rod. The rod sequences of the body wall isoforms A and B are more closely related to each other than to the pharyngeal isoforms C and D, suggesting that structural constraints have been imposed by their location within the same thick filament. We have also identified the major transcriptional start site for gene unc-54. Surprisingly, there are no TATA or other known transcription factor elements immediately upstream from the unc-54 start site, or in the upstream regions of the other genes of the C. elegans MHC gene family.

Nucleotide sequence analysis of soybean small heat shock protein genes belonging to two different multigene families

In soybean, the small heat shock proteins of 15 to 18 kDa are encoded in the nucleus by at least two different multigene families, designated class I and class VI. Genomic DNA sequences of two new heat shock genes and flanking regions were determined: Gmhsp18.5-C, a class I gene, and Gmhsp17.9-D, the first known class VI gene. Comparison of both genes revealed a moderate homology (approx. 38%) mainly within the 3' ends of their coding regions. Hydropathic characterizations and secondary-structure predictions of the deduced amino acid sequences revealed two conserved domains within the C-terminal halves of the polypeptides that are also present in related proteins of other organisms. The transcription of both genes is heat shock dependent and the mRNA start sites, as determined by S1 nuclease mapping, are located downstream from typical TATA box sequences and multiple heat shock promoter elements such as 5' CT-GAA--TTC-AG. The putative promoter regions of the genes are preceded by long tracts of repetitive sequences with a high A + T content of 79 to 89%, which are bordered by runs of "simple sequences" such as (A) 12/13, (T)10 and (TA)10. Similar characteristic features are present in the promoter and 5'-flanking regions of other soybean heat shock genes. The possible function of these distinct sequences is discussed.

Conservation in the 5' flanking sequences of transcribed members of the Caenorhabditis elegans major sperm protein gene family

The major sperm proteins (MSPs) are encoded in the Caenorhabditis genome by a multigene family with more than 50 genes dispersed in small clusters at three chromosomal loci. In spite of their dispersed locations, all of the MSP genes appear to be expressed at the same time exclusively in the testis, indicating co-ordinate temporal and spatial regulation of these dispersed genes. Many of the MSP genes must be transcribed, because RNA hybridization with gene-specific probes showed that individual genes each contribute less than 3% to the total poly(A)+ RNA, and 13 out of 14 sequenced cDNAs came from different genes. Primer extension assays from MSP mRNA showed that most of the MSP mRNAs must be initiated at position -35 from the translation start codon. Extensive similarity was found in the first 100 nucleotides of genomic sequence flanking the start codons of ten MSP genes from different chromosomal locations. All MSP genes contained a consensus ribosome binding site, a consensus TATA homology 27 nucleotides distal to the site of mRNA initiation, and ten highly conserved nucleotides adjacent to the site of initiation. All the MSP genes contained the sequence AGATCT located approximately 65 nucleotides upstream from the transcriptional start, but little or no similarity was found more distal to this. Some of these conserved sequences may be cis-acting control elements that ensure the cell and temporal specificity of transcription of these co-ordinately regulated genes.