Methods for the preparation of messenger RNA

The effects of pH and salts on nucleic acid partitioning during phenol extraction

The partitioning of nucleic acids is sensitive to pH during phenol extraction. However, the exact effects of pH on phenol extraction had not been systematically investigated, and the mechanism of which were not fully elucidated. In this paper, we showed that the partitioning of nucleic acids was determined neither solely by the pH of the aqueous buffer being used, nor by the "pH of the phenol"; the latter is a completely wrong conception. We demonstrated that a key determinant for nucleic acid partitioning during phenol extraction was the equilibrated pH of the aqueous phase, which should be defined as the pH of phenol extraction. For example, when 50 mM NaAc-HAc buffer at pH of 3.47 was mixed with an equal volume of water-saturated phenol, the equilibrated pH of aqueous phase would be raised to ∼3.84. At this pH, almost all of genomic DNA partitioned into the phenol phase, and genomic DNA-free total RNA was retained in the aqueous phase. Several salts were found affecting the partitioning of nucleic acids during phenol extraction in different manners. Based on these results, a low-cost and efficient method for genomic DNA-free total RNA extraction was developed.

Threonine-insensitive homoserine dehydrogenase from soybean: genomic organization, kinetic mechanism, and in vivo activity

Aspartate kinase (AK) and homoserine dehydrogenase (HSD) function as key regulatory enzymes at branch points in the aspartate amino acid pathway and are feedback-inhibited by threonine. In plants the biochemical features of AK and bifunctional AK-HSD enzymes have been characterized, but the molecular properties of the monofunctional HSD remain unexamined. To investigate the role of HSD, we have cloned the cDNA and gene encoding the monofunctional HSD (GmHSD) from soybean. Using heterologously expressed and purified GmHSD, initial velocity and product inhibition studies support an ordered bi bi kinetic mechanism in which nicotinamide cofactor binds first and leaves last in the reaction sequence. Threonine inhibition of GmHSD occurs at concentrations (K(i) = 160-240 mM) more than 1000-fold above physiological levels. This is in contrast to the two AK-HSD isoforms in soybean that are sensitive to threonine inhibition (K(i) approximately 150 microM). In addition, GmHSD is not inhibited by other aspartate-derived amino acids. The ratio of threonine-resistant to threonine-sensitive HSD activity in soybean tissues varies and likely reflects different demands for amino acid biosynthesis. This is the first cloning and detailed biochemical characterization of a monofunctional feedback-insensitive HSD from any plant. Threonine-resistant HSD offers a useful biotechnology tool for manipulating the aspartate amino acid pathway to increase threonine and methionine production in plants for improved nutritional content.

Stress-induced activation of the AMP-activated protein kinase in the freeze-tolerant frog Rana sylvatica

Survival in the frozen state depends on biochemical adaptations that deal with multiple stresses on cells including long-term ischaemia and tissue dehydration. We investigated whether the AMP-activated protein kinase (AMPK) could play a regulatory role in the metabolic re-sculpting that occurs during freezing. AMPK activity and the phosphorylation state of translation factors were measured in liver and skeletal muscle of wood frogs (Rana sylvatica) subjected to anoxia, dehydration, freezing, and thawing after freezing. AMPK activity was increased 2-fold in livers of frozen frogs compared with the controls whereas in skeletal muscle, AMPK activity increased 2.5-, 4.5- and 3-fold in dehydrated, frozen and frozen/thawed animals, respectively. Immunoblotting with phospho-specific antibodies revealed an increase in the phosphorylation state of eukaryotic elongation factor-2 at the inactivating Thr56 site in livers from frozen frogs and in skeletal muscles of anoxic frogs. No change in phosphorylation state of eukaryotic initiation factor-2alpha at the inactivating Ser51 site was seen in the tissues under any of the stress conditions. Surprisingly, ribosomal protein S6 phosphorylation was increased 2-fold in livers from frozen frogs and 10-fold in skeletal muscle from frozen/thawed animals. However, no change in translation capacity was detected in cell-free translation assays with skeletal muscle extracts under any of the experimental conditions. The changes in phosphorylation state of translation factors are discussed in relation to the control of protein synthesis and stress-induced AMPK activation.

Construction, database integration, and application of an Oenothera EST library

Coevolution of cellular genetic compartments is a fundamental aspect in eukaryotic genome evolution that becomes apparent in serious developmental disturbances after interspecific organelle exchanges. The genus Oenothera represents a unique, at present the only available, resource to study the role of the compartmentalized plant genome in diversification of populations and speciation processes. An integrated approach involving cDNA cloning, EST sequencing, and bioinformatic data mining was chosen using Oenothera elata with the genetic constitution nuclear genome AA with plastome type I. The Gene Ontology system grouped 1621 unique gene products into 17 different functional categories. Application of arrays generated from a selected fraction of ESTs revealed significantly differing expression profiles among closely related Oenothera species possessing the potential to generate fertile and incompatible plastid/nuclear hybrids (hybrid bleaching). Furthermore, the EST library provides a valuable source of PCR-based polymorphic molecular markers that are instrumental for genotyping and molecular mapping approaches.

Molecular and biochemical characterization of VR-EILs encoding mung bean ETHYLENE INSENSITIVE3-LIKE proteins

ETHYLENE INSENSITIVE3 (EIN3) is a transcription factor involved in the ethylene signal transduction pathway in Arabidopsis. Two full-length cDNA clones, pVR-EIL1 and pVR-EIL2, encoding EIN3-LIKE proteins were isolated by reverse transcriptase-polymerase chain reaction and by screening the cDNA library of mung bean (Vigna radiata) hypocotyls. VR-EIL1 and VR-EIL2 share 70% identity and display varying degrees of sequence conservation (39%-65%) with previously isolated EIN3 homologs from Arabidopsis, tobacco (Nicotiana tabacum) and tomato (Lycopersicon esculentum) plants. Gel retardation assay revealed that both VR-EILs were able to interact specifically with optimal binding sequence-1, the recently identified optimal binding sequence for tobacco TEIL, with the binding of VR-EIL2 being more efficient than that of VR-EIL1. Transient expression analysis using a VR-EIL::smGFP fusion gene in onion (Allium cepa) epidermal cells indicated that the VR-EIL proteins were effectively targeted to the nucleus. The fusion protein of VR-EIL2 with GAL4 DNA-binding domain strongly activated transcription of a reporter gene in yeast cells, and an essential domain for transcription-stimulating activity was localized to the amino-terminal acidic region that consists of 50 amino acid residues. In contrast with what has been previously found in EIN3- and TEIL-overexpressing Arabidopsis plants, transgenic tobacco seedlings expressing the VR-EIL genes under the control of cauliflower mosaic virus 35S promoter did not exhibit a constitutive triple response. Instead, they displayed a markedly enhanced proliferation of root hairs, one of the typical ethylene response phenotypes, and increased sensitivity to exogenous ethylene. In addition, the pathogenesis-related (PR) genes encoding beta-1,3-glucanase, osmotin, and PR1 were constitutively expressed in 35S::VR-EIL lines without added ethylene, and were hyperinduced in response to ethylene treatment. These results indicate that VR-EILs are functional in tobacco cells, thereby effectively transactivating the GCC-box-containing PR genes and enhancing sensitivity to ethylene. The possible physiological role of VR-EILs is discussed in the light of the suggestion that they are active components of the ethylene-signaling pathway and their heterologous expressions constitutively turn on a subset of ethylene responses in tobacco plants.

Structure and expression of the TREX1 and TREX2 3' --> 5' exonuclease genes

The TREX1 and TREX2 genes encode mammalian 3'-->5' exonucleases. Expression of the TREX genes in human cells was investigated using a reverse transcription-polymerase chain reaction strategy. Our results show that TREX1 and TREX2 are expressed in all tissues tested, providing direct evidence for the expression of these genes in human cells. Potential transcription start sites are identified for the TREX genes using rapid amplification of cDNA ends to recover the 5'-flanking regions of the TREX transcripts. The 5'-flanking sequences indicate transcription initiation from consensus putative promoters identified -140 and -650 base pairs upstream of the TREX1 open reading frame (ORF) and -623 and -753 base pairs upstream of the TREX2 ORF. Novel TREX1 and TREX2 cDNAs are identified that contain protein-coding sequences generated from exons positioned in genomic DNA up to 18 kilobases 5' to the TREX1 ORF and up to 25 kilobases 5' to the TREX2 ORF. These novel cDNAs and sequences in the GenBank data base indicate that transcripts containing the TREX1 and TREX2 ORFs are produced using a variety of mechanisms that include alternate promoter usage, alternative splicing, and varied sites for 3' cleavage and polyadenylation. These initial studies have revealed previously unrecognized complexities in the structure and expression of the TREX1 and TREX2 genes.

Fatty acid profiles of invertebrate iridescent viruses

Eight invertebrate iridescent viruses (IVs) from diverse host taxa were grown in a common lepidopteran host, Galleria mellonella. The lipid composition of purified virus was assessed by fatty acid methyl esterase (FAME) analysis using a gas-liquid chromatograph. IV fatty acid profiles were markedly different from those of the host tissues. The interrelationships among the IVs did not follow previous serological and genetic findings. We conclude that FAME analysis is not a useful technique for revealing phylogenetic relationships among these viruses.

cDNA cloning and characterization of lamina-associated polypeptide 1C (LAP1C), an integral protein of the inner nuclear membrane

Lamina-associated polypeptides 1A-1C (LAPs1A-1C) are related integral membrane proteins of the inner nuclear membrane that bind to both A- and B-type lamins and have a putative role in the membrane attachment and assembly of the nuclear lamina. In this study, we have cloned a cDNA encoding LAP1C. The DNA sequence predicts a 506-amino acid protein of largely hydrophilic character with a single membrane-spanning region between residues 311-333. Mapping of the epitope recognized by the anti-LAP1 monoclonal antibody RL13 indicates that the hydrophilic domain containing residues 1-310 is exposed to the nucleoplasm and thus that LAP1C is a type II integral membrane protein. A second class of LAP1 cDNAs was isolated that contains two protein-coding nucleotide insertions in the LAP1C sequence. These probably encode parts of LAPs1A and/or -1B, suggesting that LAP1 isotypes arise from alternative splicing. Immunoblot analysis of mouse P19 teratocarcinoma cells and the P19MES-differentiated derivative of the latter suggest that LAP1 isotypes are differentially expressed during development, similar to members of the nuclear lamin family. Since the different LAP1 isotypes appear to bind lamins with different affinities, these changes in expression could be important for developmentally regulated alterations in nuclear structure.

RNA transcripts of the beta-thalassaemia allele IVS-2-654 C-->T: a small amount of normally processed beta-globin mRNA is still produced from the mutant gene

IVS-2-654 C-->T is a common Chinese beta-thalassaemia mutation. Previous studies report that this mutation resulted in the formation of an abnormally spliced mRNA and the absence of detectable normal beta-globin mRNA, hence the mutation was considered to cause beta o-thalassaemia. We recently used the method of PCR amplified cDNA copies of circulating erythroid cell mRNA to analyse the mutant gene transcripts and found that this IVS-2-654 mutation does not abolish normal RNA processing entirely, but that a significant amount (over 15%) of normally processed beta-globin mRNA is produced. Microglobin chain biosynthetic analysis using the HPLC method showed that beta-globin chain was also present in the blood of patients with IVS-2-654 C-->T mutation. Accordingly, this mutant allele leads to a beta (+)-thalassaemia. Further, the methodology described in this paper provides a new approach towards the detection of RNA transcripts of beta-thalassaemia alleles as well as the study of gene expression in beta-thalassaemia and other genetic diseases.

Molecular characterisation of a novel, repetitive protein of the paraflagellar rod in Trypanosoma brucei

A partial cDNA clone, termed 5.20, was isolated from a lambda-gt11 phage expression library using a complex antiserum to the T. brucei cytoskeleton. Antisera against the fusion protein product of this 5.20 cDNA recognized a closely-spaced polypeptide doublet of high molecular weight (ca. 180-200 kDa) on immunoblots of T. brucei cytoskeletal preparations. Immunogold labelling suggested the 5.20 protein is intracellular and localized along the entire length of the paraflagellar rod. This pattern is similar to that generated with a monoclonal antibody, ROD1, which recognizes a high molecular weight protein doublet indistinguishable from that detected by 5.20-specific antisera. ROD1 recognizes mammalian spectrin, but the use of specific anti-spectrin antibodies for immunoblotting did not support ideas that 5.20 encodes spectrin or that spectrin can be specifically detected in T. brucei by such methods. Moreover, the sequence of the 5.20 cDNA insert bears little similarity, either in its nucleotide or predicted amino acid sequence to other known proteins and appears to be a unique cytoskeletal protein characterized especially by sequential amino acid sequence repetitiveness. The location of this novel protein suggests it may be responsible for providing either paraflagellar rod-membrane links or for organizing the more abundant paraflagellar rod structural proteins.

Identification of placental form of glutathione S-transferase in ACNU-resistant murine glioma cell lines

Expression of the placental form of glutathione S-transferase (GST-P) in 1-(4-amino-2-methyl-5-pyrimidinyl) methyl-3-(2-chloro-ethyl)-3-nitrosourea hydrochloride (ACNU)-sensitive 9L and C6 glioma cells, and ACNU-resistant 9L (9LR) and C6 (C6R) glioma cells was investigated by Northern blot analysis for GST-P mRNA and Western blot analysis for GST-P protein. The sensitivity of 9L, 9LR, C6 and C6R cell lines to ACNU was evaluated by microculture tetrazolium assay. Localization of GSTP-P protein in these cell lines was investigated by immunocytochemical method. Expression level of GST-P mRNA in 9LR cells was 3 times that of 9L cells and the level of GST-P protein in 9LR cells was 1.7 times that of 9L cells. On the contrary, the amount of GST-P mRNA of C6R cells was 1.3-fold larger than C6 cells and that of GST-P protein of C6R cells was 1.3-fold larger than C6 cells. Immunocytochemical investigation revealed that 9LR cells had stronger expression of GST-P in their cytoplasm than 9L cells. Expression of GST-P in both C6R and C6 cells was less than 9L and 9LR cells, and the amount was similar to each other. The present study suggests that GST-P may play an important role in detoxification of anti-cancer drugs in some glioma cells.

Alternative splicing of HLA-G transcripts yields proteins with primary structures resembling both class I and class II antigens

We have investigated HLA-G mRNA expression in cells and tissues expressing the gene. This analysis has demonstrated that the HLA-G primary transcript is alternatively spliced to yield at least three distinct mature mRNAs. Sequencing of the transcripts has shown that the largest mRNA is essentially that previously characterized, encoding a leader sequence, three external domains, a transmembrane region, and a cytoplasmic sequence. Of the two smaller messages, a 900-base mRNA does not include exon 3, resulting in a predicted protein sequence with the alpha 1 and alpha 3 external domains joined. The smallest mRNA results from splicing out exons 3 and 4, connecting the alpha domain directly to the transmembrane sequence. Alternative splicing of HLA-G mRNA was found in placental tissues and in eye tissue as well as in HLA-G-transfected cell lines. In term placental tissue the smallest mRNA appeared to be more abundant than the full-length form, while in a cell line derived from an earlier developmental stage the larger form predominated. Immunoprecipitation of [35S]methionine-labeled cell lysates showed that three different HLA-G proteins were present in transfected cells, with sizes corresponding to those predicted from the three alternative mRNA sequences. These findings are discussed in terms of potential functions of the alternative HLA-G proteins.

Polymorphism at the HLA-E locus predates most HLA-A and -B polymorphism

The extensive polymorphism of the classic class I antigens has been well described. In contrast, the nonclassic HLA antigens are distinguished by their low polymorphism. We examine here the HLA polymorphism of the HLA-E locus by examining the DNA sequence of cDNA from nine ethnically diverse individuals. From this analysis, we show that there is no polymorphism in the regions including exon 1 and from exon 4 to exon 8, the 3' untranslated exon. In exons 2 and 3, there are two base substitutions, one of which is at a replacement site and the other silent. The replacement substitution changes an arginine to a glycine at position 107, defining two alleles at the HLA-E locus. Using the PCR on exon 3 from genomic DNA and hybridization with oligonucleotide probes, we have examined 90 HLA-typed individuals to determine the relative frequency of the two alleles in the population and their association with the classical antigens. This analysis showed that these two alleles were present at nearly equal frequencies in the population. Surprisingly, both alleles were found in an essentially random association with all but one HLA-A and -B haplotype. The single exception was to the A1-B8 haplotype, which appeared to be linked to only one of the two alleles. One implication of this random association is that these HLA-E alleles may have existed before most of the HLA-A and B polymorphism. Thus, selection has maintained the HLA-E locus essentially unaltered during a time when considerable polymorphism was being selected for at the HLA-A and -B loci. This finding may also have important consequences in an unrelated bone marrow transplant, where it is predicted that 37% of HLA-A and -B matched donors are mismatched at the HLA-E locus.

Genomic rearrangements in human rotavirus strain Wa; analysis of rearranged RNA segment 7

Two rotavirus variants containing genomic rearrangements were isolated from human rotavirus strain Wa. In one variant (H5) the rearrangement involves the RNA segment 5, while in the other variant (H57) two genes, 5 and 7 are rearranged. The rearranged genes are composed exclusively of sequences from the genes they substitute. Sequence analysis of the rearranged segment 7 indicated that it is a partial duplication of the wild type gene, in a head-to-tail orientation.

The specific production of the third component of complement by osteoblastic cells treated with 1 alpha,25-dihydroxyvitamin D3

A 190 kDa protein was purified from conditioned media of mouse marrow-derived stromal cell (ST2) cultures treated with 1 alpha,25-dihydroxyvitamin D3 (1 alpha,25(OH)2D3) and identified as the third component of mouse complement (C3). Northern and Western blot analysis revealed that the production of C3 by ST2 and primary osteoblastic cells was strictly dependent on 1 alpha,25(OH)2D3, but the production by hepatocytes was not. Adding 1 alpha,25(OH)2D3 together with mouse C3 antibody to bone marrow cultures greatly inhibited the formation of tartrate-resistant acid phosphatase (TRAP)-positive osteoclast-like multinucleated cells. Adding C3 alone induced no TRAP-positive cell formation. These results suggest that, in bone tissues, C3 is specifically produced by osteoblasts in response to 1 alpha,25(OH)2D3 and somehow involved in inducing differentiation of bone marrow cells into osteoclasts in concert with other factors produced by osteoblasts in response to 1 alpha,25(OH)2D3.

Expression of glutathione S-transferase-pi messenger RNA in human esophageal cancers

The expression of human glutathione S-transferase-pi (GST-pi) in resected primary esophageal tumors and in matching normal esophageal mucosa from 25 patients undergoing radical surgery was measured by RNA blot hybridization. The RNA transcript levels of GST-pi in the tumor tissues were higher than those in normal tissues in 20 of 25 cases (80%). The mean GST-pi mRNA value in the tumor tissues (n = 25) was significantly (P less than 0.01) elevated as compared with that in background mucosa (n = 29), and in ten of 25 tumors (40%) the level of GST-pi mRNA exceeded the mean normal tissue value by two standard deviations (normal mean value + 2 X SD). The results obtained from the current experiment thus suggests that GST-pi might be a useful marker for human esophageal cancer. No correlation between GST-pi mRNA level and clinical stage or histologic characteristics was apparent.

Separation of translationally active mRNAs by reversed-phase ion-pair high-performance liquid chromatography

An ion-pair high-performance liquid chromatographic method on C4 columns was developed for the separation of mRNAs. The addition of methylmercuric hydroxide markedly influenced the separation according to length of these molecules. A method is given to recover minute amounts of translatable mRNA from the organic phase. The resolution of mRNAs improved with increasing pore size of the column support.

Transcriptional activation of cellular oncogenes fos, jun, and myc by human cytomegalovirus

The mechanisms responsible for the human cytomegalovirus (HCMV)-induced increase in cellular oncogene RNAs for c-jun, c-fos, and c-myc in human embryo lung cells (I. Boldogh, S. AbuBakar, and T. Albrecht, Science 247:561-564, 1990) were investigated. Results of transcription assays indicated that the rapid increase in RNA levels for the above-noted oncogenes was controlled at the transcriptional level and was related to enhanced transcription. The maximum rates of transcription for c-jun and c-fos genes occurred at 40 min postinfection, while for the c-myc gene the maximum rate occurred at about 60 min. The magnitude of HCMV-induced activation of these cellular genes was similar to the activation induced by serum. The half-lives of the cellular oncogenes showed similar decay rates after either serum or HCMV activation when measured by dactinomycin chase. The half-life for c-fos or c-jun was about 20 min, and that for c-myc was about 40 min. Furthermore, inhibition of the RNA increase by dactinomycin or by alpha-amanitin suggested that the increase in RNA levels was due to an increase in the transcriptional activity of oncogenes triggered by HCMV.

Interleukin 1 regulates the expression of osteopontin mRNA by osteoblasts

Osteopontin is a matrix protein which belongs to the integrin superfamily and is involved in cell adhesion. In the present study, we examined the regulation of the mRNA expression of osteopontin by interleukin 1 alpha (IL-1 alpha) in osteoblasts. IL-1 alpha greatly increased the steady-state level of osteopontin mRNA in both a mouse osteoblastic cell line (MC3T3-E1) and mouse primary osteoblast-like cells. The increase in the osteopontin mRNA expression by IL-1 alpha was dose-dependent at a range of 0.004-0.2 nM. This was most likely due to an increase in the transcriptional rate, not to an increase in the stability of osteopontin mRNA. The in vitro nuclear transcription experiment showed that IL-1 alpha-treated MC3T3-E1 cells increased the synthesis of osteopontin mRNA. Besides IL-1 alpha, tumor necrosis factor alpha (TNF-alpha), lipopolysaccharides (LPS) and 1 alpha,25-dihydroxyvitamin D3 (1 alpha,25(OH)2D3) increased the osteopontin mRNA expression in both the clonal osteoblasts (MC3T3-E1) and the primary osteoblast-like cells. In response to such bone-resorbing agents, primary osteoblast-like cells expressed osteopontin mRNA much more strongly than primary fibroblast-like cells isolated from mouse calvaria. Both IL-1 alpha and 1 alpha,25(OH)2D3 greatly increased the production of 68 and 62 kDa phosphoproteins in conditioned media of MC3T3-E1 cell cultures, which probably correspond to osteopontin. These results suggest that osteopontin plays an important role in bone remodeling, in particular bone resorption.

Identification, localization, and primary structure of CAP-23, a particle-bound cytosolic protein of early development

We report the identification of CAP-23, a novel particle-bound cytosolic protein associated with developing cells in both mammalian and avian tissues. CAP-23 was a substrate for purified protein kinase C (PKC) in vitro, and the protein was phosphorylated in a PMA-sensitive manner in cultured cells, indicating that it is a PKC substrate in situ. cDNA coding for chick CAP-23 was isolated. The deduced sequence revealed an unusual amino acid composition that strikingly resembled that of rat GAP-43, a growth-associated neuron-specific PKC substrate. Further predicted features of CAP-23 included a PKC phosphorylation site at Ser-6, and the presence of basic NH2- and COOH-terminal domains. CAP-23 was encoded by an mRNA of approximately 1.5 kb, whose distribution during chick development resembled that of the corresponding protein. Southern blot analysis revealed the presence of a single main hybridizing species in the chick genome. The distribution of CAP-23 during development was analyzed with Western blots and by immunofluorescence on tissue sections. In cultured cells the protein appeared to be distributed in a regular spotted pattern below the entire cell surface. In early chick embryos (E2), CAP-23 was present in most if not all cells. The protein then became progressively restricted to only some developing tissues and to only certain cells in these tissues. In most tissues CAP-23 levels fell below detection limits between E15 and E19. Highest levels of the protein were found in the nervous system, where CAP-23 levels peaked around E18, and where elevated levels were still detectable at birth.

Evolutionary transfer of the chloroplast tufA gene to the nucleus

Evolutionary gene transfer is a basic corollary of the now widely accepted endosymbiotic theory, which proposes that mitochondria and chloroplasts originated from once free-living eubacteria. The small organellar chromosomes are remnants of larger bacterial genomes, with most endosymbiont genes having been either transferred to the nucleus soon after endosymbiosis or lost entirely, with some being functionally replaced by pre-existing nuclear genes. Several lines of evidence indicate that relocation of some organelle genes could have been more recent. These include the abundance of non-functional organelle sequences of recent origin in nuclear DNA, successful artificial transfer of functional organelle genes to the nucleus, and several examples of recently lost organelle genes, although none of these is known to have been replaced by a nuclear homologue that is clearly of organellar ancestry. We present gene sequence and molecular phylogenetic evidence for the transfer of the chloroplast tufA gene to the nucleus in the green algal ancestor of land plants.

Human leukocyte antigen F (HLA-F). An expressed HLA gene composed of a class I coding sequence linked to a novel transcribed repetitive element

We describe here the isolation and sequencing of a previously uncharacterized HLA class I gene. This gene, HLA-5.4, is the third non-HLA-A,B,C gene characterized whose sequence shows it encodes an intact class I protein. RNase protection assays with a probe specific for this gene demonstrated its expression in B lymphoblastoid cell lines, in resting T cells, and skin cells, while no mRNA could be detected in the T cell line Molt 4. Consistent with a pattern of expression different from that of other class I genes, DNA sequence comparisons identified potential regulator motifs unique to HLA-5.4 and possibly essential for tissue-specific expression. Protein sequence analysis of human and murine class I antigens has identified 10 highly conserved residues believed to be involved in antigen binding. Five of these are altered in HLA-5.4, and of these, three are nonconservative. In addition, examination of the HLA-5.4 DNA sequence predicts that the cytoplasmic segment of this protein is shorter than that of the classical transplantation antigens. The 3' untranslated region of the HLA-5.4 gene contains one member of a previously undescribed multigene family consisting of at least 30 members. Northern analysis showed that several of these sequences were transcribed, and the most ubiquitous transcript, a 600-nucleotide polyadenylated mRNA, was found in all tissues and cells examined. This sequence is conserved in the mouse genome, where a similar number of copies were found, and one of these sequences was also transcribed, yielding a 600-nucleotide mRNA. The characterization of this unique HLA class I gene and the demonstration of its tissue-specific expression have prompted us to propose that HLA-5.4 be designated HLA-F.

Isolation and sequence of four small nuclear U RNA genes of Trypanosoma brucei subsp. brucei: identification of the U2, U4, and U6 RNA analogs

Trypanosomes use trans splicing to place a common 39-nucleotide spliced-leader sequence on the 5' ends of all of their mRNAs. To identify likely participants in this reaction, we used antiserum directed against the characteristic U RNA 2,2,7-trimethylguanosine (TMG) cap to immunoprecipitate six candidate U RNAs from total trypanosome RNA. Genomic Southern analysis using oligonucleotide probes constructed from partial RNA sequence indicated that the four largest RNAs (A through D) are encoded by single-copy genes that are not closely linked to one another. We have cloned and sequenced these genes, mapped the 5' ends of the encoded RNAs, and identified three of the RNAs as the trypanosome U2, U4, and U6 analogs by virtue of their sequences and structural homologies with the corresponding metazoan U RNAs. The fourth RNA, RNA B (144 nucleotides), was not sufficiently similar to known U RNAs to allow us to propose an identify. Surprisingly, none of these U RNAs contained the consensus Sm antigen-binding site, a feature totally conserved among several classes of U RNAs, including U2 and U4. Similarly, the sequence of the U2 RNA region shown to be involved in pre-mRNA branchpoint recognition in yeast, and exactly conserved in metazoan U2 RNAs, was totally divergent in trypanosomes. Like all other U6 RNAs, trypanosome U6 did not contain a TMG cap and was immunoprecipitated from deproteinized RNA by anti-TMG antibody because of its association with the TMG-capped U4 RNA. These two RNAs contained extensive regions of sequence complementarity which phylogenetically support the secondary-structure model proposed by D. A. Brow and C. Guthrie (Nature [London] 334:213-218, 1988) for the organization of the analogous yeast U4-U6 complex.

Isolation and characterization of a mammalian gene encoding a high-affinity cAMP phosphodiesterase

A rat brain cDNA library has been constructed in a Saccharomyces cerevisiae expression vector and used to isolate genes that can function in yeast to suppress the phenotypic effects of RAS2val19, a mutant form of the RAS2 gene analogous to an oncogenic mutant of the human HRAS gene. One cDNA, DPD, was cloned and its genetic and biochemical properties were characterized. A DPD product would share 80% amino acid sequence identity with the Drosophila melanogaster dunce-encoded protein over an extended region. We have shown that the DPD protein is a high-affinity cAMP-specific phosphodiesterase.

Isolation and sequence of four small nuclear U RNA genes of Trypanosoma brucei subsp. brucei: identification of the U2, U4, and U6 RNA analogs

Trypanosomes use trans splicing to place a common 39-nucleotide spliced-leader sequence on the 5' ends of all of their mRNAs. To identify likely participants in this reaction, we used antiserum directed against the characteristic U RNA 2,2,7-trimethylguanosine (TMG) cap to immunoprecipitate six candidate U RNAs from total trypanosome RNA. Genomic Southern analysis using oligonucleotide probes constructed from partial RNA sequence indicated that the four largest RNAs (A through D) are encoded by single-copy genes that are not closely linked to one another. We have cloned and sequenced these genes, mapped the 5' ends of the encoded RNAs, and identified three of the RNAs as the trypanosome U2, U4, and U6 analogs by virtue of their sequences and structural homologies with the corresponding metazoan U RNAs. The fourth RNA, RNA B (144 nucleotides), was not sufficiently similar to known U RNAs to allow us to propose an identify. Surprisingly, none of these U RNAs contained the consensus Sm antigen-binding site, a feature totally conserved among several classes of U RNAs, including U2 and U4. Similarly, the sequence of the U2 RNA region shown to be involved in pre-mRNA branchpoint recognition in yeast, and exactly conserved in metazoan U2 RNAs, was totally divergent in trypanosomes. Like all other U6 RNAs, trypanosome U6 did not contain a TMG cap and was immunoprecipitated from deproteinized RNA by anti-TMG antibody because of its association with the TMG-capped U4 RNA. These two RNAs contained extensive regions of sequence complementarity which phylogenetically support the secondary-structure model proposed by D. A. Brow and C. Guthrie (Nature [London] 334:213-218, 1988) for the organization of the analogous yeast U4-U6 complex.

Identity of the immunoglobulin heavy-chain-binding protein with the 78,000-dalton glucose-regulated protein and the role of posttranslational modifications in its binding function

The 78,000-dalton glucose-regulated protein (GRP78) and the immunoglobulin heavy-chain-binding protein (BiP) were shown to be the same protein by NH2-terminal sequence comparison. Immunoprecipitation of GRP78-BiP induced by glucose starvation and a temperature-sensitive mutation in a hamster fibroblast cell line demonstrated the association of GRP78-BiP with other cellular proteins. In both fibroblasts and lymphoid cells, GRP78-BiP was found to label with 32Pi and [3H]adenosine. Phosphoamino acid analysis demonstrated that GRP78-BiP is phosphorylated on serine and threonine residues. Conditions which induce increased production of GRP78-BiP resulted in decreased incorporation of 32Pi and [3H]adenosine into GRP78-BiP. Furthermore, we report here that the phosphorylated form of BiP resides in the endoplasmic reticulum and that BiP which is associated with heavy chains is not phosphorylated or labeled with [3H]adenosine, whereas free BiP is. This suggests that posttranslational modifications may be important in regulating the synthesis and binding of BiP.

Identity of the immunoglobulin heavy-chain-binding protein with the 78,000-dalton glucose-regulated protein and the role of posttranslational modifications in its binding function

The 78,000-dalton glucose-regulated protein (GRP78) and the immunoglobulin heavy-chain-binding protein (BiP) were shown to be the same protein by NH2-terminal sequence comparison. Immunoprecipitation of GRP78-BiP induced by glucose starvation and a temperature-sensitive mutation in a hamster fibroblast cell line demonstrated the association of GRP78-BiP with other cellular proteins. In both fibroblasts and lymphoid cells, GRP78-BiP was found to label with 32Pi and [3H]adenosine. Phosphoamino acid analysis demonstrated that GRP78-BiP is phosphorylated on serine and threonine residues. Conditions which induce increased production of GRP78-BiP resulted in decreased incorporation of 32Pi and [3H]adenosine into GRP78-BiP. Furthermore, we report here that the phosphorylated form of BiP resides in the endoplasmic reticulum and that BiP which is associated with heavy chains is not phosphorylated or labeled with [3H]adenosine, whereas free BiP is. This suggests that posttranslational modifications may be important in regulating the synthesis and binding of BiP.

Characterization of the rat mas oncogene and its high-level expression in the hippocampus and cerebral cortex of rat brain

The human mas oncogene was originally detected by its ability to transform NIH 3T3 cells. We previously showed that the protein encoded by this gene is unique among cellular oncogene products in that it has seven hydrophobic potential transmembrane domains and shares strong sequence similarity with a family of hormone-receptor proteins. We have now cloned the rat homolog of the mas oncogene, determined its DNA sequence, and examined its expression in various rat tissues. A comparison of the predicted sequences of the rat and human mas proteins shows that they are highly conserved, except in their hydrophilic amino-terminal domains. Our examination of the expression of mas, determined by RNA-protection studies, indicates that high levels of mas RNA transcripts are present in the hippocampus and cerebral cortex of the brain, but not in other neural regions or in other tissues. This pattern of expression and the similarity of mas protein to known receptor proteins suggest that mas encodes a receptor that is involved in the normal neurophysiology and/or development of specific neural tissues.

Import of rat liver mitochondrial transhydrogenase

The biosynthesis of pyridine dinucleotide transhydrogenase has been studied in isolated rat hepatocytes and in a rabbit reticulocyte-lysate translation system supplemented with either intact isolated rat liver mitochondria or the soluble matrix fraction from isolated mitochondria. In intact hepatocytes, the transhydrogenase precursor was short-lived in the cytosol and was efficiently imported into the membranous fraction. When the cell-free translation mixture was incubated with intact mitochondria, the transhydrogenase precursor was processed to the mature form, to an extent that depended on the amount of added mitochondria. Incubation of the translation mixture with the soluble mitochondria matrix fraction converted the precursor to a mature-sized protein with 75% efficiency, this being blocked by various proteinase inhibitors such as EDTA, 1,10-phenanthroline and leupeptin.

Glucocorticoid regulation of insulin receptor gene transcription in IM-9 cultured lymphocytes

We have reported that glucocorticoids increase steady state insulin receptor mRNA levels in target cells. In the present study using IM-9 cultured human lymphocytes, we investigated the mechanism responsible for this glucocorticoid mediated increase in insulin receptor mRNA levels. Incubation of IM-9 cells with 100 nM dexamethasone for 4 h stimulated a parallel increase in both polysomal and nuclear insulin receptor RNAs indicating that glucocorticoids did not alter the nuclear transport of insulin receptor RNA. Dexamethasone did not alter insulin receptor mRNA half life (t 1/2 = 140 +/- 20 min), indicating that glucocorticoids did not influence mRNA stability. Furthermore, the dexamethasone-induced increase in insulin receptor mRNA levels was not blocked by pretreatment of cells with cycloheximide indicating that the glucocorticoid effect was independent of new protein synthesis. When the labeled transcripts from nuclear run-off incubations were then hybridized to immobilize human insulin receptor cDNA, a three- to fourfold increase in transcriptional activity was observed. This transcriptional effect occurred before the increase in steady state insulin receptor mRNA levels and over the same range of dexamethasone concentrations. These studies indicate therefore a direct effect of glucocorticoids on insulin receptor gene transcription, and demonstrate that the insulin receptor gene is under hormonal control.

A rapid method for isolation of double stranded RNA

A rapid and simple method for the isolation and purification of dsRNA is presented. The crucial step of this method is the extraction of proteins and DNA with acid phenol. After the extraction, only RNA is left in the aqueous phase. ssRNA contamination of the RNA preparation can be greatly reduced when ammonium sulfate is present during the extraction.

Heat shock triggers rapid protein phosphorylation in soybean seedings

Heat shock arrests the synthesis of many cellular proteins and simultaneously initiates expression of a unique set of proteins, termed heat shock proteins. We have found that heat shock rapidly triggers phosphorylation of a set of proteins in soybean seedlings. Although the kinetics of phosphorylation and the heat shock response are similar, the major identified phosphorylation products do not comigrate with heat shock proteins on polyacrylamide gels. Cadmium, which is known to induce the heat shock response, stimulates phosphorylation of the same set of proteins. The rapidity of phosphorylation suggests that it may play a pivotal role in sensing and transducing elevated temperature stress in plants.

Phytochrome-mediated regulation of β-amylase mRNA level in mustard (Sinapis alba L.) cotyledons

Phytochrome, activated by continuous red light, increases the amount of total polyadenylated RNA during photomorphogenesis of mustard (Sinapis alba L.) cotyledons. In-vitro translation of total polyadenylated RNA in a reticulocyte translation system has shown that the activity of translatable β-amylase mRNA is increased by phytochrome about threefold in the 3-d-old cotyledons, based on equal amounts of polyadenylated RNA, and about eightfold on a per-cotyledon basis. Cordycepin prevents the accumulation of translatable β-amylase mRNA. It is concluded that the phytochrome-mediated control of β-amylase synthesis is exerted on the level of mRNA synthesis. During seedling development in continuous red light, a phytochrome-dependent increase of β-amylase mRNA can be observed at least 6 h before the onset of β-amylase synthesis. If, after a period of enzyme synthesis, phytochrome action is interrupted by long-wavelength far-red light followed by darkness, β-amylase mRNA as well as β-amylase synthesis remain at a high level for 8-10 h and then decline sharply. It is concluded that β-amylase mRNA, having an apparent lifetime of the order of 8-10 h, can be formed under the influence of phytochrome during early seedling development but it activates β-amylase synthesis only after a lag-phase of about 8 h, when the cotyledons acquire competence to synthesize the enzyme. The consequences of these findings for the signal-transduction chain of phytochrome are discussed.

Low temperature causes accumulation of unspliced fibroin mRNA precursor molecules in silkworm larvae

Silk fibroin premessenger mRNA is a large (17 kb) molecule containing a single intron. Previous S1 mapping studies yielded evidence of processing cleavages at sites within the intron, in addition to the major cleavages at the intron/exon boundaries. We have performed S1 mapping experiments using RNA from animals which had been incubated at low temperature. These experiments show a marked accumulation of full-length fibroin mRNA precursor relative to controls, and a reduction in the abundance of molecules lacking portions of the intron. These results demonstrate a partial uncoupling of transcription and splicing in vivo.

Apparent generation of a segmented mRNA from two separate tandem gene families in Trypanosoma cruzi

Using a cDNA for an abundant Trypanosoma cruzi mRNA as probe, we have cloned and sequenced a gene which is organized in at least 20 nearly perfect tandem repeats of 940 base pairs. The 5' end of the mRNA has been sequenced by primer extension and found to contain a 35 nucleotide mini-exon (or spliced-leader) sequence that is ubiquitous in trypanosome mRNAs. This sequence, however, is not present in the tandem genomic repeats which encode the exon containing the major portion of the mRNA. Previous studies have shown that the 35-nucleotide sequence is encoded by a separate tandem gene family. One model to explain the formation of a segmented mRNA invokes priming of transcription by a small RNA which contains the leader sequence at its 5' end. However, northern blot analysis of total trypanosome RNA reveals a ladder of molecules larger than the mature mRNA, which appear to be faithful multimeric copies of the tandem gene. The discrete sizes of these RNAs correspond to those expected for partially processed precursors. These observations lend credence to the possibility of an alternative model where segmented mRNAs are generated by inter-molecular splicing.

Differential import and processing of the precursors to F1-ATPase beta-subunit and ornithine carbamyltransferase by liver, spleen, heart and kidney mitochondria

The cytoplasmically made subunits 2 (beta) and 3 (gamma) of the H+-ATPase from mammalian mitochondria are synthesized in vitro as larger polypeptides. In contrast, pre-cytochrome c could not, on the basis of its molecular weight, be distinguished from the mature polypeptide. This was shown by programming a reticulocyte lysate with rat heart RNA and immunoprecipitating the labeled translation products with polypeptide-specific antibodies. When a translated lysate containing the precursor to the beta-subunit was incubated with isolated rat spleen mitochondria, it was converted to the mature subunit and was no longer susceptible to externally added trypsin. The conversion to the mature form occurred in the absence of protein synthesis. This post-translational maturation process of the beta-subunit was more efficient when carried out with spleen or liver mitochondria than with heart or kidney mitochondria. The converse relative efficiency was observed when the processing of the precursor to ornithine carbamyltransferase by these mitochondria was examined. These results indicate that mitochondria do not discriminate against tissue-specific mitochondrial proteins. In addition, the observed varying degrees of efficiency of mitochondria from different tissues in importing and processing these two precursors suggest that the activity of precursor(s)-specific translocation-maturation systems varies between different types of mitochondria.