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Eukaryotic mRNAs encoding abundant and scarce proteins are statistically dissimilar in many structural features.

It is well known that non-coding mRNA sequences are dissimilar in many structural features. For individual mRNAs correlations were found for some of these features and their translational efficiency. However, no systematic statistical analysis was undertaken to relate protein abundance and structural characteristics of mRNA encoding the given protein. We have demonstrated that structural and contextual features of eukaryotic mRNAs encoding high- and low-abundant proteins differ in the 5' untranslated regions (UTR). Statistically, 5' UTRs of low-expression mRNAs are longer, their guanine plus cytosine content is higher, they have a less optimal context of the translation initiation codons of the main open reading frames and contain more frequently upstream AUG than 5' UTRs of high-expression mRNAs. Apart from the differences in 5' UTRs, high-expression mRNAs contain stronger termination signals. Structural features of low- and high-expression mRNAs are likely to contribute to the yield of their protein products.

5' Untranslated Regions↗

Expression of a cDNA for a neuronal calcium channel alpha 1 subunit enhances secretion from adrenal chromaffin cells.

A synthetic oligonucleotide was used to isolate mouse brain cDNA clones coding for a brain isoform of the alpha 1 subunit of the voltage-sensitive Ca2+ channel. Twenty-six independent cDNA clones were isolated and sequenced. All the cDNA clones reported here showed high homology to the rat brain class C cDNA sequence (Snutch, T. P., Tomlinson, W. J., Leonard, J. P., and Gilbert, M. M. (1991) Neuron 7, 45-57). Comparison of the individual mouse brain class C (mbC) cDNA sequences indicated the presence of four regions within the alpha 1 subunit coding sequence where alternative splicing can take place in mouse brain and raise the possibility that combinatorial arrangement of these splice variants could give rise to a heterogenous class of mbC transcripts. Northern blot analysis demonstrated that mbC mRNA sequences could be detected in highest abundance in mouse heart, at lower levels in mouse brain and spinal cord, and not at all in liver or skeletal muscle. An expression vector for one isoform of the mbC alpha 1 subunit cDNA was constructed using the human cytomegalovirus promoter to direct expression, and this expression vector was used in a novel transfection assay of primary cultures of bovine adrenal chromaffin cells. Transfection of the mbC alpha 1 subunit expression vector increased the secretion of human growth hormone derived from a cotransfected human growth hormone expression vector after stimulation with elevated K+ or the dihydropyridine agonist, Bay K8644. These experiments suggest that this isoform of the mbC alpha 1 subunit is functional in the transfected chromaffin cells and that the number of Ca2+ channels is a limiting component in the secretion from chromaffin cells in culture.

Adrenal Medulla↗

Characterization of lipopolysaccharide-induced macrophage gene expression.

A cDNA library from LPS-treated murine peritoneal macrophages has been screened by differential hybridization with radiolabeled cDNA from untreated and LPS-treated macrophages. Six clones hybridizing with mRNA sequences present in LPS-treated cells but not in controls were selected for further characterization. When the recombinant bacteriophage DNA from each clone was used as a probe in Northern analysis of total RNA from LPS-treated macrophages, inducible mRNA ranging from 1.45 to 6.4 kb were seen. In five of six cases, the mRNA expression was undetectable in untreated macrophage cultures. All but one clone identified mRNA that were inducible even in the presence of cycloheximide, indicating the independence of such gene expression from protein synthesis; none of the genes were superinduced by this treatment. The time course of expression differed among the individual genes. Four were induced transiently, whereas two showed stable increasing accumulation through an 8-h period after stimulation. In addition, four of the genes were seen within 30 min of stimulation, whereas two were seen only after 2 to 4 h. Two genes were induced only by treatment with LPS, whereas four were also induced in response to other agents, including IFN-gamma, macrophage CSF, and PMA. The insert sequences from these recombinant clones did not hybridize with a set of cDNA encoding other inducible gene products, including TNF, IL-1, ornithine decarboxylase, c-myc, c-fos, JE, or KC. Thus, these six cDNA appear to encode inducible macrophage genes that are distinct from one another as well as from a selection of previously described early genes. Although their functional identity remains indeterminate, they may encode previously described early proteins induced in macrophages treated with LPS.

Animals↗

RNA interference silencing the transcriptional message: aspects and applications.

RNA interference (RNAi) is silencing of gene expression by double-stranded RNA (dsRNA) having complementary sequence to the target gene to be silenced. This phenomenon has transformed into a complete technology for functional genomic studies. Small interfering RNAs (siRNAs) are 21- to 23-nucleotide dsRNAs, in which the sense strand is the same as the target mRNA and the antisense strand is the complement of the target mRNA sequence. These are the effector molecules for inducing RNAi, leading to posttranscriptional gene silencing with RNA-induced silencing complex. Besides siRNA, which can be chemically synthesized, various other systems in the form of potential effector molecules for posttranscriptional gene silencing are available, such as short hairpin RNAs (shRNAs), long dsRNAs, short temporal RNAs, and micro RNAs (miRNAs). These effector molecules either are processed into siRNA such as in the case of shRNA or directly aid gene silencing as in the case of miRNA. RNAi for various unknown genes may facilitate to elucidate inherited genetic diseases and provide drug candidates for viral and oncogenic diseases. This can be achieved by targeting mRNA from oncogenic genes or mRNA for viral cellular receptor and viral structural proteins for RNAi. In this article, we evaluate various aspects and applications of RNAi technology and provide comprehensive information for the system currently available for inducing RNAi.

Agriculture↗

Amino acid sequence of a chicken heat shock protein derived from the complementary DNA nucleotide sequence.

The complete nucleotide sequence for a chicken heat shock protein (hsp108) was determined from cDNA clones isolated from hen oviduct and bursal lymphoma recombinant DNA libraries. This protein has certain biochemical similarities to the progesterone receptor, but it is clearly distinct from it. The initial cDNA clone, isolated from a chicken oviduct cDNA library, was detected by antibody screening and hybrid-selected translation [Zarucki-Schulz, T., Kulomaa, M. S., Headon, D. R., Weigel, N. L., Baez, M., Edwards, D. P., McGuire, W. L., Schrader, W. T., & O'Malley, B. W. (1984) Proc. Natl. Acad. Sci. U.S.A. 81, 6358-6362]. The earlier clones were used to screen for additional cDNAs, and cDNAs that define the entire mRNA sequence of hsp108 have been obtained. The nucleotide sequence codes for peptides present in hsp108 as determined by protein microsequencing. The 5' end of the mRNA was determined by primer extension studies. The mRNA contains a noncoding region of 101 nucleotides upstream from the predicted initiation codon. The 3' untranslated region contains 244 nucleotides beyond the termination codon, and it contains a predicted polyadenylation signal 26 nucleotides from the end of the complete cDNA. The coding region of 2385 nucleotides corresponds to a polypeptide chain of 795 amino acids, giving a molecular weight of 91,555 for the hsp108 protein. In another paper, evidence is presented that hsp108 shows a high degree of amino acid sequence homology with two heat shock proteins, hsp90 (yeast) and hsp83 (Drosophila), and is indeed inducible by heat shock [Sargan, D. R., Tsai, M.-J., & O'Malley, B. W. (1986) Biochemistry (following paper in this issue)].

Amino Acid Sequence↗

A common myosin light chain is expressed in chicken embryonic skeletal, cardiac, and smooth muscles and in brain continuously from embryo to adult.

We have isolated cDNA clones of the mRNA for chick embryonic myosin light chain (MLC), L23, by cross-hybridization with chicken skeletal muscle MLC1 cDNA. The identification of the isolated cDNAs was carried out by in vitro translation of hybrid-selected mRNA. Sequence analysis of the cloned cDNAs revealed that the cDNA insert contained 832 nucleotides and predicted a polypeptide of 185 amino acids with a calculated molecular weight of 20,687. The deduced amino acid sequence for L23 showed high sequence similarities to those of adult alkali type MLCs from various tissues, indicating that L23 belongs to the alkali MLC group. Using the cloned cDNA as a hybridization probe, we have revealed by RNA blot analysis that the expression of L23 mRNA was regulated in temporal and tissue-specific manners. The L23 mRNA of 1.1 kilobases is transiently expressed in embryonic skeletal, cardiac, and smooth muscles of chickens. It is also found in the brain of chickens during all stages of development so far investigated. Only a single gene for L23 was detected by Southern blot of chick genomic DNA. We therefore suggest that L23 is expressed from a single gene in both embryonic muscles and brain.

Age Factors↗

Interactions of mRNAs and gRNAs involved in trypanosome mitochondrial RNA editing: structure probing of an mRNA bound to its cognate gRNA.

Posttranscriptional editing of trypanosome mitochondrial messenger RNA is directed by small guide RNAs (gRNAs). Using crosslinking techniques, we have previously shown that the gRNA base pairs to the mRNA via a 5' anchor, whereas its 3' U-tail interacts with upstream purine-rich mRNA sequences. The incorporation of crosslinking data into RNA folding programs produced similar structure predictions for all gRNA/mRNA pairs examined. This suggests that gRNA/mRNA pairs can form common secondary structure motifs that may be important for recognition by the editing complex. In this study, the structure of CYb mRNA crosslinked to gCYb-558 was examined using solution-probing techniques. The mRNA/gRNA crosslinked molecules are efficient substrates for gRNA-directed cleavage. In addition, when the cleavage assay is performed in the presence or absence of additional UTP, the activities of both the U-specific exonuclease and terminal uridylyl transferase (tutase) can be detected. These results indicate that a partial editing complex can assemble and function on these substrates suggesting that the crosslink captured the molecules in a biologically relevant interaction. The structure probing data directly show that the U-tail protects several mRNA bases predicted to be involved in the U-tail-mRNA duplex. In combination with our previous studies, these new data provide additional support for the predicted secondary structure of interacting gRNA/mRNA pairs.

Animals↗

PCR isolation and cloning of novel splice variant mRNAs from known drug target genes.

Alternative splicing of pre-mRNAs is an important mechanism for the generation of vertebrate protein diversity. Unfortunately, the contribution of alternative splicing to protein diversity is currently not well understood because many full-length mRNA sequences have yet to be identified. In this report, we describe the use of RT-PCR to identify and clone 279 novel alternatively spliced mRNAs from 114 well-known drug target genes. Our findings demonstrate the existence of many novel alternatively spliced mRNA transcripts and suggest that many more genes undergo functionally significant alternative splicing than previously thought.

Alternative Splicing↗

Screening of the entire coding region of p53 in low grade lymphoproliferative disorders.

This report details a rapid method for screening the entire p53 coding region (exons 2-11). This method, based on the non-isotopic RNase cleavage assay, uses novel primer sequences and an adaptation of the MutationScreener method. A mutation in 20% of the sample was easily detectable by this method, whereas mutations below 50% were undetectable using the original method. Alterations to the wild-type p53 mRNA sequence were found in nine of the 130 patients with low grade lymphoproliferative disorders screened, and this was confirmed by DNA sequencing in eight of eight samples. The method is a simple and reliable technique for screening for p53 mutations.

Genes, p53↗

Transition from embryonic to adult transcription pattern of serotonin N-acetyltransferase gene in avian pineal gland.

The study reports the change of transcription pattern of serotonin N-acetyltransferase gene and melatonin receptor genes during ontogenesis of the avian pineal gland. The RT-PCR technique was used to investigate the expression of the arylalkylamine N-acetyltransferase (AA-NAT) and melatonin receptor genes during development of the pineal glands isolated from Japanese quail (Coturnix coturnix japonica) embryos incubated from 3 days on until hatching (17 days), and in some organs (pineal, brain hemisphere, eye, leg, heart) of the 3-day-old quail embryo. It was shown that two phases of AA-NAT expression are observed during pineal gland development. The first, embryonic-type phase, lasts from the beginning until 7-10 days of incubation, and is marked by the presence of two RT-PCR products for AA-NAT: the shorter mature form without intron (238 bp), and the longer form (323 bp) containing an unprocessed intron of 85 bp. The second, adult-type phase is characterized by the presence of a single mature transcript, containing no intron; it starts from 7 to 10 days of incubation and lasts until hatching and in the adult pineal. The duration of this transition time from the embryonic to the adult transcription pattern in the quail pineal gland from 7 to 10 days of incubation we attribute to asynchronic embryo development, because quail chicks usually hatch between the 16th and 19th day of incubation. Analysis of the AA-NAT protein sequences for chick and quail (GeneBank accession no. U 46 502 and AF 007 068, respectively) revealed their perfect homology with the part of protein read from the sequence present in the adult-type phase of the pineal gland (the RT-PCR product of 238 bp). The presence of the intron (in the 323 bp RT-PCR product, accession no. AY 197 460) in the embryonic-phase of the pineal gland changes the reading frame of the mRNA sequence and the hypothetical resulting protein loses its homology with the chick and quail AA-NAT enzyme starting with 105th amino acid of the complete chick AA-NAT protein comprising 205 amino acids (accession no. U 46 502). In the whole embryos at stages 1-8 (according to the Hamburger-Hamilton classification) both RT-PCR products with and without intron were consistently found, and individual tissues from 3-day-old embryos also produced two AA-NAT products, i.e., the expression was of the embryonic-type. At the time of transition from the embryonic to the adult AA-NAT transcription pattern, in 7-11-day-old embryos, all three melatonin receptor transcripts (mel-1a, mel-1b, and mel-1c) were observed in the pineals, without consistent modifications of the band intensity. In the adult pineal, a single mature AA-NAT transcript was present as well as all three melatonin receptor transcripts, usually with preferential expression of the mel-1a band. The transition time from the embryonic to adult AA-NAT expression pattern coincides well with the acquisition of functional activity and the appearance of melatonin synthesis in the embryonic pineal reported for chicken, as related to quail. We suggest that the change in transcription pattern of the AA-NAT gene may reflect another, still unknown mechanism of regulating AA-NAT activity during ontogenesis, at the level of mRNA processing, whose specificity (or not) for embryonic development we wish to establish in the future.

Animals↗

Regulation of in vitro expression of the Escherichia coli frd operon: alanine and Fnr represent positive and negative control elements.

The frdABCD operon of Escherichia coli encodes the anaerobically expressed terminal electron transport enzyme, fumarate reductase. Two mutually exclusive hairpin loop structures can occur in frdmRNA just downstream of the start of the frdA cistron. The mRNA sequence involved encodes a stretch of sequence rich in Ala and uses all four of the codons for this amino acid. In vitro expression of the frdABCD operon showed that as the level of plasmid DNA was increased from 150 fmol to 225 fmol, transcription of mRNA was suddenly elevated 6.5-fold, consistent with the concept of titrating out a repressor protein. Further studies showed that the concomitant 10.9-fold increase in translation of protein was heavily biased towards the proximal end of the operon, with little or no expression of FrdC or FrdD and a ratio of FrdA:FrdB of 2.6:1. Addition of Ala to the S-30 extract caused a 6.1-fold amplification of frd messenger transcription, a 17.6-fold increase in Frd protein translation, and a balancing of the subunit ratios to 1:1:1:1. The expression of the bla gene carried on the plasmid was not affected by DNA titration or the addition of Ala. When fnr DNA was added in equimolar ratio to frdDNA the amplification of fumarate reductase expression by Ala was abolished and the ratio of subunits produced showed a high degree of polarity with or without Ala.

Alanine↗

Alpha heavy chain disease alpha mRNA contain nucleotide sequences of unknown origins.

Human alpha heavy chain disease is characterized by the production of abnormally short alpha IgH chains. In previously published cases it has been found that the malignant cells produce abnormal alpha mRNA, lacking VH and CH1 sequences and composed of a leader sequence peptide, sequences of variable length (69 to 84 bp) and of unknown origin, followed by normal CH2 and CH3 sequences. In this study we established the nucleotide sequence of alpha mRNA for six cases of alpha heavy chain disease. We observed that all six alpha mRNA lack the VH and CH1 sequences as do those previously described. They also contain in-frame inserts of unknown origin between the leader peptide and the normal CH2 and CH3 coding sequences. These inserts are of variable length (42 to 105 bp) and they are unrelated. These results suggest the existence of a common mechanism defect leading to deletions/insertions in alpha heavy chain disease rather than a specific interaction between alpha 1 IgH gene with a unique defined molecular species.

Amino Acid Sequence↗

The 3alpha-hydroxy-steroid-dehydrogenase-mRNA and -protein are more prevalent in pericentral than in periportal hepatocytes.

BACKGROUND: Under physiological conditions, de-novo synthesis and metabolism of bile acids are confined mainly to the pericentral zone of the liver acinus. In the rat, 3alpha-hydroxy-steroid-dehydrogenase (3alpha-HSD) is the major bile acid-binding protein. At the same time, this protein is involved in the de-novo synthesis and metabolism of bile acids. Because bile acid processing is greater in the pericentral than in the periportal region, we investigated whether 3alpha-HSD is more prevalent in the pericentral than in the periportal area. DESIGN: We determined the 3alpha-HSD-protein and its mRNA in periportal and pericentral rat cells. METHOD: Rat hepatocytes from the periportal or pericentral areas were isolated using the digitonin perfusion technique. For Northern blotting, a labelled 1.3-kb cDNA insert corresponding to the mRNA sequence of 3alpha-HSD was used. For Western blotting, a polyclonal rabbit antiserum against human 3alpha-HSD was used. Blots were quantified by densitometry using phosphoimaging. RESULTS: The amounts of the 3alpha-HSD-protein and its mRNA were significantly greater in the pericentral than in the periportal cells. CONCLUSIONS: The greater occurrence of 3alpha-HSD in pericentral than in periportal hepatocytes is in line with the concept that bile acid synthesis and metabolism take place predominantly in pericentral cells.

3-Hydroxysteroid Dehydrogenases↗

Transcriptional regulation of the tryptophan oxygenase gene in rat liver by glucocorticoids.

The enzyme tryptophan oxygenase (EC 1.13.11.11), which is synthesized in rat liver, is induced by glucocorticoids. We have used cloned tryptophan oxygenase genomic and cDNA sequences to study the mechanism of induction. Rat liver poly(A+) RNA was separated on a formaldehyde gel, blotted to nitrocellulose, and hybridized to a nick-translated tryptophan oxygenase cDNA clone to analyze the kinetics of tryptophan oxygenase mRNA accumulation. Transcription in isolated rat liver nuclei was investigated to determine the relative rate of transcription of the tryptophan oxygenase gene. Analysis of the accumulation of albumin mRNA, which is unaffected by glucocorticoids, served as an internal control. We show here that the synthetic glucocorticoid dexamethasone causes a 10-fold increase in the concentration of tryptophan oxygenase mRNA sequences in rat liver, and that this is a consequence of transcriptional activation of the tryptophan oxygenase gene.

Animals↗

Biosensor for the specific detection of a single viable B. anthracis spore.

A simple membrane strip-based biosensor for the detection of viable B. anthracis spores was developed and combined with a spore germination procedure as well as a nucleic acid amplification reaction to identify as little as one viable B. anthracis spore in less than 12 h. The biosensor is based on identification of a unique mRNA sequence from the anthrax toxin activator (atxA) gene encoded on the toxin plasmid, pXO1. Preliminary work relied on plasmid vectors in both E. coli and B. thuringiensis expressing the atxA gene. Once the principle was firmly established, the vaccine strain of B. anthracis was used. After inducing germination and outgrowth of spores of B. anthracis (Sterne strain), RNA was extracted from lysed cells, amplified using nucleic acid sequence-based amplification (NASBA), and rapidly identified by the biosensor. While the biosensor assay requires only 15-min assay time, the overall process takes 12 h for the detection of as little as one viable B. anthracis spore, and is shortened significantly, if larger amounts of spores are present. The biosensor is based on an oligonucleotide sandwich-hybridization assay format. It uses a membrane flow-through system with an immobilized oligonucleotide probe that hybridizes with the target sequence. Signal amplification is provided when the target sequence hybridizes to a second oligonucleotide probe that has been coupled to dye-encapsulating liposomes. The dye in the liposomes then provides a signal that can be read visually or quantified with a hand-held reflectometer. The biosensor can detect as little as 1.5 fmol of target mRNA. Specificity analysis revealed no crossreactivity with closely related species such as B. cereus, B. megaterium, B. subtilis, B. thuringiensis etc.

Bacillus anthracis↗

Cloning and sequence analysis of mRNA for mouse aspartate aminotransferase isoenzymes.

The nucleotide sequences of mRNAs for the mouse mitochondrial and cytosolic aspartate aminotransferase isoenzymes (mAspAT and cAspAT) (EC 2.6.1.1) were determined from complementary DNAs. The mAspAT mRNA comprises minimally 2460 nucleotides and codes for a polypeptide of 430 amino acid residues corresponding to the precursor form of the mAspAT (pre-mAspAT). The cAspAT mRNA comprises minimally 2086 nucleotides and codes for a polypeptide of 413 amino acid residues. The region coding for the mature mAspAT and that for the cAspAT show about 53% overall homology. The former shares 49% and the latter 48% of homology, respectively, with that of the Escherichia coli aspC gene, which has been shown to code for the E. coli AspAT (Kuramitsu, S., Okuno, S., Ogawa, T., Ogawa, H., and Kagamiyama, H. (1985) J. Biochem. (Tokyo) 97, 1259-1262). When the deduced amino acid sequence of the mouse pre-mAspAT was compared with that of the pig pre-mAspAT polypeptide, we found that they share a 94% homology and that the mouse pre-mAspAT yields a presequence consisting of 29 amino acid residues and a mature mAspAT, consisting of 401 amino acid residues. These numbers and the amino acid residues present at the putative cleavage site are all in complete agreement in these two species. The deduced amino acid sequence of the mouse cAspAT shares 91% homology with that of the pig cAspAT. Comparisons of the nucleotide and deduced amino acid sequences between the mouse and E. coli AspATs suggest that the mammalian mAspAT gene is more closely related to the E. coli aspC gene than is the mammalian cAspAT gene.

Amino Acid Sequence↗

The muscular dysgenesis mutation in mice leads to arrest of the genetic program for muscle differentiation.

Muscular dysgenesis (mdg) is a mutation in mice which causes the failure of excitation-contraction coupling in skeletal muscle. Although the sarcolemma, the sarcoplasmic reticulum, and the contractile apparatus all maintain nearly normal function, sarcolemmal depolarization fails to cause calcium release from the sarcoplasmic reticulum. Recently, the primary genetic defect in this mutation was shown to be located in the structural gene for the dihydropyridine receptor. We have examined the developmental expression from Fetal Day 15 onward, in normal and mutant muscle, of several unidentified genes as well as genes which are known markers of muscle differentiation. We find that the majority of mRNA sequences are found at similar concentrations in normal and dysgenic muscles at birth. Many differentiation-related genes also are expressed at normal levels early during myogenesis in mutant mice. However, as late fetal development progresses in dysgenic muscle, the mRNA concentrations for these genes fail to undergo the rapid rise which is characteristic of normal muscle. Several additional, unidentified genes, which normally would be down-regulated during development, remain expressed at a high level in dysgenic muscle. Thus, the primary absence of a functional dihydropyridine receptor appears to prevent the changes in gene expression which are necessary for maturation of skeletal muscle.

Actins↗

Molecular basis of an adult form of Sandhoff disease: substitution of glutamine for arginine at position 505 of the beta-chain of beta-hexosaminidase results in a labile enzyme.

Sandhoff disease is a lysosomal storage disorder characterized by accumulation of GM2 ganglioside due to mutations in the beta-chain of beta-hexosaminidase. Hexosaminidase activity is negligible in infantile Sandhoff disease whereas residual activity is present in juvenile and adult forms. Here we report the molecular basis of the first described adult form of Sandhoff disease. Southern analysis of chromosomal DNA indicated the absence of chromosomal deletions in the gene encoding the beta-chain. Northern analysis of RNA from cultured fibroblasts demonstrated that at least one of the beta-chain alleles was transcribed into normal-length mRNA. Sequence analysis of the entire cDNA prepared from poly-adenylated RNA showed that only one point mutation was present, consisting of a G-->A transition at nucleotide position 1514. This mutation changes the electric charge at amino acid position 505 by substitution of glutamine for arginine in a highly conserved part of the beta-chain, present even in the slime mold Dictyostelium discoideum. The nucleotide transition generated a new restriction site for DdeI, which was present in only one of the alleles of the patient. Reverse transcription of mRNA followed by restriction with DdeI resulted in complete digestion at the mutation site, demonstrating that the second allele was of an mRNA-negative type. Transfection of COS cells with a cDNA construct containing the mutation but otherwise the normal sequence resulted in the expression of a labile form of beta-hexosaminidase. These results show that the patient's is a genetic compound, and that the lability of beta-hexosaminidase found in this form of Sandhoff disease is based on a single nucleotide transition.

Amino Acid Sequence↗