Methylmercury hydroxide enhancement of translation and transcription of ovalbumin and conalbumin mRNA's

Signalling to eIF4E in cancer

Translational control plays a critical role in the regulation of gene expression in eukaryotes and affects many essential cellular processes, including proliferation, apoptosis and differentiation. Under most circumstances, translational control occurs at the initiation step at which the ribosome is recruited to the mRNA. The eukaryotic translation initiation factor 4E (eIF4E), as part of the eIF4F complex, interacts first with the mRNA and facilitates the recruitment of the 40S ribosomal subunit. The activity of eIF4E is regulated at many levels, most profoundly by two major signalling pathways: PI3K (phosphoinositide 3-kinase)/Akt (also known and Protein Kinase B, PKB)/mTOR (mechanistic/mammalian target of rapamycin) and Ras (rat sarcoma)/MAPK (mitogen-activated protein kinase)/Mnk (MAPK-interacting kinases). mTOR directly phosphorylates the 4E-BPs (eIF4E-binding proteins), which are inhibitors of eIF4E, to relieve translational suppression, whereas Mnk phosphorylates eIF4E to stimulate translation. Hyperactivation of these pathways occurs in the majority of cancers, which results in increased eIF4E activity. Thus, translational control via eIF4E acts as a convergence point for hyperactive signalling pathways to promote tumorigenesis. Consequently, recent works have aimed to target these pathways and ultimately the translational machinery for cancer therapy.

Local and global factors affecting RNA sequencing analysis

High-throughput RNA sequencing (RNA-seq) continues to provide unparalleled insight into transcriptome complexity. Now the "gold standard" for assessing global transcript levels, RNA-seq is poised to revolutionize our understanding of transcription and posttranscriptional regulation of RNA. Despite significant advantages over prior experimental strategies, RNA-seq is not without pitfalls. We have identified a number of confounding factors that significantly affect sequencing coverage. These include regional GC content, preferential sites of fragmentation, and read "pile-up" due to primer affinity and transcript end effects. Independent of cell type and laboratory, when ignored, these factors can bias analyses. Understanding the underlying principles responsible for producing these artifacts is key to recognizing both their presence and how their effects may be controlled. Here we outline the causes of and strategies to avoid several previously unreported complicating factors common to RNA-seq experiments.

Thermostabilization and thermoactivation of thermolabile enzymes by trehalose and its application for the synthesis of full length cDNA

The advent of thermostable enzymes has led to great advances in molecular biology, such as the development of PCR and ligase chain reaction. However, isolation of naturally thermostable enzymes has been restricted to those existing in thermophylic bacteria. Here, we show that the disaccharide trehalose enables enzymes to maintain their normal activity (thermostabilization) or even to increase activity at high temperatures (thermoactivation) at which they are normally inactive. We also demonstrate how enzyme thermoactivation can improve the reverse transcriptase, reaction. In fact, thermoactivated reverse transcriptase, which displays full activity even at 60 degrees C, was powerful enough to synthesize full length cDNA without the early termination usually induced by stable secondary structures of mRNA.

Virus-like particles in Eimeria nieschulzi are associated with multiple RNA segments

RNA preparations from sporulated oocysts of Eimeria nieschulzi were found to contain 2 double-stranded RNA segments of 5.0 kb and 5.7 kb that were not present in other species of Eimeria. Treatment of crude lysates with RNase A revealed that in addition to these two segments, 3 other segments of 0.57 kb, 0.72 kb and 11.5 kb were protected from digestion, suggesting that they were enclosed within particles. Virus-like particles with a diameter of approximately 39 nm were purified by caesium chloride buoyant density centrifugation. Four of the five RNA segments copurified with these particles. In keeping with the nomenclature generally adopted for protozoan viruses, we have named this new isolate ENV 1. The largest RNA segment does not cosediment with ENV 1 particles and may be derived from another RNA-protein complex that is unstable under the conditions used. The particle size and genome structure of ENV 1 both differ from that of the Eimeria stiedae virus (ESV), which is the only other virus to have been isolated from Eimeria to date. Short cDNA clones derived from ENV 1 show significant homology to a region of the Leishmania virus (LRV 1) genome that encodes an RNA-dependent RNA polymerase. The polymerase sequences from ENV 1 and LRV 1 are more closely related to each other than to any other protein sequences in the GenEMBL Database. This raises intriguing questions about the origins of the two viruses, since Eimeria and Leishmania normally infect different hosts and also show different cell tropisms within these hosts.

Translation inhibition by an mRNA coding region secondary structure is determined by its proximity to the AUG initiation codon

In the present study we investigate the impact of highly stable coding region secondary structures on mRNA translation efficiency. By introducing antisense segments into the 3'non-translated region of human alpha-globin mRNA we are able to synthesize a series of transcripts in which site-specific secondary structures are introduced without altering the primary structure of the 5' non-translated region, the coding region, or the encoded protein product. Coding region duplexes in close proximity to the AUG initiation codon are found to inhibit translation severely to a degree equal to that of a duplex that extends into the 5' non-translated region. In contrast, mRNAs containing duplexes positioned further 3' in the coding region translate at levels that are significantly higher although are still below those of native alpha-globin mRNA. The primary determinant of translation inhibition by coding region duplexes appears to be the proximity of the duplex to the AUG initiation codon and reflects a parallel inhibition of monosome formation. These data demonstrate that extensive coding region secondary structures suppress translation to a minimal or to a substantial degree depending on their distance from the initiation codon.

Transcription of the rat cholecystokinin gene is initiated at multiple sites: verification by an in vitro transcription system

The cDNA that accommodates the most distal 5'-end region of cholecystokinin mRNA was isolated from an internally primed cDNA library. Using primer extension and S1 nuclease protection analyses, we demonstrated multiple RNA molecules generated from the rat cholecystokinin gene, a single-copy sequence. The longest RNA is transcribed at position--225 upstream relative to the translation start site. The major transcription, more than 95% of the total cholecystokinin mRNA in rat brain, occurred at--59 and its promoter activity was determined by in vitro RNA synthesis in a HeLa cell extract. Deletion to--105 demonstrated an approximately 60% decrease in transcriptional level compared with the full promoter activity. At least the upstream region between--254 and--105 is necessary for transcription initiated at--59 of the cholecystokinin gene by the cell-free system.

Translation of hepatitis A virus RNA in vitro: aberrant internal initiations influenced by 5' noncoding region

Hepatitis A virus (HAV) RNAs were translated in vitro in rabbit reticulocyte lysates. The pattern of proteins synthesized from full-length HAV RNA was highly complex, consisting of a continuous spectrum of polypeptides ranging from less than 20,000 to greater than 200,000 Da. The pattern was not significantly altered by varying incubation times, ion, or other reaction parameters, or by the addition of HeLa or BS-C-1 cell extracts to the translation reactions. Plasmids engineered with mutations in the 3C coding region produced transcripts which directed the synthesis of the same overall pattern of polypeptide products as those transcribed from wild-type sequences, suggesting that protein processing by 3C did not generate the complex set of protein products. Translation of RNA containing only the P3 coding region of HAV, directly adjacent to the HAV 5' noncoding region, generated a set of protein products which precisely matched a subset of those synthesized from full-length HAV RNA. The translation products of P3 RNA, full-length RNA, and mutant 3C-containing RNAs were analyzed by immunoprecipitation with antisera specific for 3D, VP1, and 2C sequences; several products were subjected to N-terminal sequence analysis. All together, the results demonstrate that translation of HAV RNA in rabbit reticulocyte lysates initiates predominantly at a large number of internal AUG codons, especially those in the P3 coding region. A minor population of products is initiated from sites in the P1 and P2 regions. The latter proteins undergo some proteolytic processing, at unidentified sites, catalyzed by 3C protein sequences. Replacement of the HAV 5' noncoding region with encephalomyocarditis virus 5' end sequences increased initiation at the correct polyprotein start site and both reduced and altered the products generated by internal initiation.

Cloning and characterization of a cDNA for the B beta chain of rat fibrinogen: evolutionary conservation of translated and 3'-untranslated sequences

A cDNA clone for the B beta chain of rat fibrinogen has been isolated and characterized. The cDNA insert is 1023 bp in length and corresponds to the 3' half of the B beta chain mRNA. The cDNA represents 890 bp of the coding sequence for the C-terminal half of the B beta chain and 133 bp of the 3'-untranslated region. The coding sequence for this region of the rat cDNA shares a high degree of identity with the corresponding regions of the human and bovine B beta-chain cDNAs and a moderate degree of identity with the corresponding region of the lamprey B beta-chain cDNA. A comparison of the amino acid sequences deduced from these cDNAs reveals three regions which share extensive identity among all four sequences. Two additional regions are identified which share extensive identity among the three mammalian sequences and significant identity with the lamprey sequence. These regions appear to represent distinct functional domains. Possible functions for these domains are briefly discussed. A high degree of identity also exists between the 3'-untranslated regions of the three mammalian cDNAs, suggesting that this region of the mRNA, although noncoding, is functionally important.

Intraviral homology and subgenomic RNAs of pepper ringspot virus

The Tobraviruses constitute a group of rod-shaped, bipartite, plus-stranded RNA viruses. We report on homologies between the two viral genomic RNA molecules of pepper ringspot virus (PRV) and on the subgenomic components generated from them during infection. It has previously been shown that the 3'-terminal 459 nucleotides of PRV RNA-1 and RNA-2 are identical. Here it is shown that there is a second homology between RNA-1 and a region of RNA-2, located at least 240 nucleotides downstream from its 5' terminus. In agreement with strains in another Tobravirus group, we observe three subgenomic components in extracts of plants infected with PRV. Two of these, RNAs-1a (1.6 kb) and -1b (0.8 kb), are derived from RNA-1 (the larger genomic RNA). They are probably mRNAs for 29- and 16-kDa nonstructural virus proteins. The smaller genomic RNA, RNA-2, generates the subgenomic component RNA-2a (1.3-1.45 kb) which is probably an efficient capsid protein mRNA. Previously reported subgenomic components of 2.8 and 1.1 kb are shown to be electrophoretic artifacts. RNA-2a, but not 1a or 1b, is present in virion RNA preparations, indicating that it is the only subgenomic species to be encapsidated.

Fetal and variant alpha-fetoproteins are encoded by mRNAs that differ in sequence at the 5' end

The temperature-sensitive RLA209-15 fetal rat hepatocyte line grown at the nonpermissive temperature (40 degrees C, normal phenotype) produces authentic rat alpha-fetoproteins (AFPs) of 69K and 73K (fetal AFPs) which are encoded by a 2.2-kb mRNA. These cells also produce low levels of a 1.7-kb AFP mRNA and a 65K variant AFP when grown at the permissive temperature (33 degrees C, transformed phenotype). Hybrid-selected translation demonstrates that the 1.7-kb AFP mRNA encodes the 65K variant AFP. Northern blot hybridization and S1 nuclease analyses indicate that the 1.7-kb mRNA lacks sequences present in the first seven 5' exons of the 2.2-kb AFP mRNA. However, the 1.7- and 2.2-kb AFP mRNAs share common sequences extending from the beginning of the eighth exon (corresponding to nucleotide 873 of the fetal AFP mRNA) to the 3' end. Primer extension analysis suggests that the 1.7-kb RNA contains additional sequences 5' to the common regions shared by both AFP mRNAs. We have previously shown that adult rat liver produces a 1.7-kb AFP mRNA; we now report the isolation of a cDNA (ARFP5) encoding this variant AFP mRNA from an adult rat liver cDNA library. Restriction endonuclease mapping and sequence analysis of ARFP5 confirm that the 1.7- and 2.2-kb AFP mRNAs share similar sequences at the 3' region (approximately 1.1 kb). However, ARFP5 contains an additional 90 bp variant AFP mRNA-specific 5' sequence which is located in the seventh intron of the rat AFP gene.(ABSTRACT TRUNCATED AT 250 WORDS)

Human submandibular gland statherin and basic histidine-rich peptide are encoded by highly abundant mRNA's derived from a common ancestral sequence

The molecular cloning of sequences encoding human submandibular gland (SMG) statherin and a basic histidine-rich peptide is described. The corresponding mRNA's were highly abundant in the human and the Rhesus monkey (Macaca mulatta) SMG, but no homologous message was detectable in the murine SMG. Sequence analysis revealed strong homology between the statherin and basic histidine-rich mRNA's, suggesting their evolution from a common ancestral sequence.

Relationship between two major immunoreactive forms of arginase in Neurospora crassa

Two major immunoreactive proteins of Mr 41,700 and 36,100 have been detected in crude mycelial extracts with polyclonal antibodies raised against arginase purified from Neurospora crassa. The latter corresponded to the protein used to obtain the antibodies. Both polypeptides were either missing or present in very low amounts in mutant strains having little or no detectable arginase activity. The relative proportion of the two species was altered in strains containing the nitrogen catabolite regulatory mutation nit-2. Peptide mapping indicated that the two species are very closely related, but several of the peptides which appeared to be identical by staining reacted differently with the antibodies. Both species were produced by in vitro translation of poly(A)+ mRNA, although the larger species was produced to a much smaller extent than was expected from its abundance in vivo. The results suggest the existence of multiple forms of arginase in N. crassa which differ in their response to nitrogen catabolite regulation.

Synthesis of long viral complementary DNA from 7.5 Kb poly A+ RNA templates

The poly A+ RNA of the WW and GDVII virus isolates, belonging to the Theiler's murine encephalomyelitis virus group, were used as templates for cDNA synthesis. Since several secondary structures were present along these viral RNAs the reverse transcriptase was prematurely displaced from the RNA templates and only short cDNA molecules could be synthesized. Therefore a reliable and reproducible procedure for the synthesis of long cDNA transcripts, that can be directly used for cloning into respective plasmid or phage vectors, was developed. The precise conditions and kinetics of the several enzymatic reactions were studied. The use of methylmercury hydroxide for first strand synthesis, a correct choice of Klenow polymerase for second strand synthesis and the use of vertical gel electrophoresis in combination with zone centrifugation for removal of the excess linkers were found to be of paramount importance for the synthesis of long, up to intact, 7.5 Kb cDNA transcripts.

On the specificity of antisense RNA to arrest in vitro translation of mRNA coding for Drosophila hsp 23

The specificity of action of antisense RNA for one of Drosophila low molecular weight heat shock proteins (hsp 23) was tested at the translational level using the rabbit reticulocyte lysate cell-free system. T7 polymerase-driven transcripts of hsp 23 in the antisense orientation were mixed with mRNA from heat-shocked cells under various stringency conditions prior to translation in vitro. Although the four small hsps show considerable sequence homology in their coding sequences, antisense hsp 23 RNA was shown to specifically inhibit hsp 23 mRNA translation under both high (formamide, 45 degrees C) and low stringency (37 degrees C) conditions. This suggests that the 5' leader and the ribosome binding region of mRNA are of prime importance in the specificity of action of antisense RNA at the translational level.

Enteric coronavirus TGEV: partial sequence of the genomic RNA, its organization and expression

The sequence of the 3'-most 8300 nucleotides of the genome RNA of the Purdue-115 strain of the transmissible gastroenteritis virus TGEV, a porcine coronavirus, was determined from cDNA clones. The available sequence corresponds to the part of the genome (total length greater than 20 kb) expressed through subgenomic mRNAs. The 5 subgenomic and the genomic RNA species detected in TGEV-infected cells form a 3'-coterminal 'nested' structure, a unique feature of Coronaviridae. The transcription initiation site of the TGEV subgenomic RNAs appears to involve the hexameric sequence 5'CTAAAC, which is present upstream from each coding region. In addition to the previously identified genes encoding the three structural proteins, E2, E1 and N, two regions, X1 and X2, corresponding to the non-overlapping portion of mRNAs 4 and 3, may code for so far unidentified non-structural polypeptides. The predicted X1 polypeptide (9.2 kDa) is highly hydrophobic. The sequence of the X2 region allows the translation of two non-overlapping products, i.e., X2a (7.7 kDa) and X2b (18.8 kDa). No RNA species liable to express the extreme 3' open reading frame X3 was found.

Altered sensitivity of protein synthesis to paromomycin in extracts from aging human diploid fibroblasts

Age-related differences in the effects of paromomycin (Pm) on protein synthesis have been investigated in translation reactions with extracts derived from young and old human diploid fibroblasts. Translation products from reactions directed by endogenous or exogenous mRNA were analyzed by polyacrylamide gel electrophoresis and fluorography. The exogenous mRNA lacked codons for cysteine, and therefore cysteine incorporation into translation products represented translational error. This laboratory has previously used this assay to show that the basal translational error level in the absence of Pm increases in extracts from old fibroblasts. In this report, Pm stimulated the misincorporation of cysteine by 6-7 fold over cysteine misincorporation levels in the absence of Pm. This degree of Pm stimulation was similar in extracts from young and old fibroblasts. However, other results showed quantitative differences in the responses to Pm between young and old cell extracts. Old cell extracts were less sensitive to the stimulation of the rate of protein synthesis, and more sensitive to the inhibition of protein synthesis, by Pm. It is proposed that aging human diploid fibroblasts contain altered ribosomes which react differently with Pm.

A vector-primer-cloner-sequencer plasmid for the construction of cDNA libraries: evidence for a rat glyceraldehyde-3-phosphate dehydrogenase-like mRNA and a ferritin mRNA within testis

We have developed a vector-primer-cloner-sequencer (VPCS), based on the pUC plasmids, which is easy to prepare. Stable cDNA libraries have been generated from human, rat, and bull testis. The inserts are of various size classes, including high-molecular-weight reverse transcripts which can be easily sequenced. The utility of this VPCS has been demonstrated by isolating a rat ferritin and glyceraldehyde-3-phosphate dehydrogenase-like clone.

Characterization of messenger RNA from the cerebral cortex of control and Alzheimer-afflicted brain

A detailed comparative study of RNA transcripts isolated from the neocortex of control and Alzheimer postmortem brains was made to determine whether morphological changes in the chromatin of Alzheimer neurons and glia, which we reported earlier, are accompanied by changes in the products of transcription. A number of parameters were determined including the yields of total and mRNA per gram of tissue, the relative proportions of polyadenylated [poly(A)+] mRNA in the total RNA, the size distribution of the transcripts and the length of their poly(A) tails, and the nature of their in vitro translation products. The levels of endogenous RNase activity were also measured. The effect of the agonal process on the transcript complement was examined by Northern blotting of a cloned human heat-shock cDNA to total human brain RNA. Our results reveal that the yields of total RNA, unadenylated mRNA, and poly(A) tail lengths from Alzheimer neocortex samples do not differ significantly from those of control and non-Alzheimer dementia neocortex. On the other hand we find a significant reduction in the levels and proportion of poly(A)+ mRNA in the Alzheimer samples as compared to control brain samples. Quantitative rather than qualitative differences were observed in the in vitro translation products when programmed with control and Alzheimer mRNA. No differences were found in the levels of RNase activity between control and Alzheimer samples. Heat-shock mRNA transcripts were detected in brain samples from patients in whom fever was associated with death. The direct correlation of reduced poly(A)+ mRNA and chromatin condensation in Alzheimer neocortex suggests a cause-and-effect relationship. Whether all transcribed genes are affected or only a specific subset has yet to be determined.

Synthesis of epidermal growth factor (EGF) receptor in vitro using SP6 RNA polymerase-transcribed template mRNA

The epidermal growth factor (EGF) receptor plays a key role in the control cellular proliferation, and its homology to the avian erythroblastosis virus erb B oncogene implicates its involvement in cellular transformation. The establishment of a correlation between the various structural domains of the EGF receptor and their functional counterparts would greatly advance our understanding of these processes. To this end, we have constructed an expression vector containing the SP6 viral promoter and an adjacent cDNA fragment encoding the full-length EGF receptor. Upon addition of SP6 RNA polymerase, this DNA is capable of generating large amounts of EGF receptor mRNA; this RNA can then be translated in vitro into immunoprecipitable EGF receptor protein. The translational efficiency of this EGF receptor RNA was found to be relatively low: approx. 100-fold lower than globin RNA synthesized using SP6 RNA polymerase. Use of these tools should now permit the synthesis and analysis of mutated EGF receptor protein in an effort to clarify the role of this receptor in growth control.

Rapid expression of novel proteins in goldfish retina following optic nerve crush

Polyadenylated messenger RNA was isolated from goldfish retinas at various times following unilateral crush of the optic nerve. RNA was translated in a cell-free system and product proteins analyzed by two-dimensional gel electrophoresis and autofluorography. Poly(A)+ mRNA-directed protein synthesis revealed an 8-fold increase in the labeling of polypeptides of about 30 kd Mr and a pI of 5.5 in retinas 2 d following optic nerve crush, compared with control retina mRNA translation products. In vitro labeling of retinal proteins revealed the enhanced synthesis of comparable 30 kd proteins in 2 d post-crush retinas. Evidence presented suggests that this 30 kd protein cluster may correspond to fish 30 kd stress or heat-shock proteins (hsp-30).

Existence of distinct sodium channel messenger RNAs in rat brain

The sodium channel is a voltage-gated ionic channel essential for the generation of action potentials. It has been reported that the sodium channels purified from the electric organ of Electrophorus electricus (electric eel) and from chick cardiac muscle consist of a single polypeptide of relative molecular mass (Mr) approximately 260,000 (260K), whereas those purified from rat brain and skeletal muscle contain, in addition to the large polypeptide, two or three smaller polypeptides of Mr 37-45K. Recently, we have elucidated the primary structure of the Electrophorus sodium channel by cloning and sequencing the DNA complementary to its messenger RNA. Despite the apparent homogeneity of the purified sodium channel preparations, several types of tetrodotoxin (or saxitoxin) binding sites or sodium currents have been observed in many excitable membranes. The occurrence of distinguishable populations of sodium channels may be attributable to different states of the same channel protein or to distinct channel proteins. We have now isolated complementary DNA clones derived from two distinct rat brain mRNAs encoding sodium channel large polypeptides and present here the complete amino-acid sequences of the two polypeptides (designated sodium channels I and II), as deduced from the cDNA sequences. A partial DNA sequence complementary to a third homologous mRNA from rat brain has also been cloned.

Regulation of protein synthesis in virus-infected animal cells

This chapter summarizes the structural features that govern the translation of viral mRNAs: where the synthesis of a protein starts and ends, how many proteins can be produced from one mRNA, and how efficiently. It focuses on the interplay between viral and cellular mRNAs and the translational machinery. That interplay, together with the intrinsic structure of viral mRNAs, determines the patterns of translation in infected cells. It also points out some possibilities for translational regulation that can only be glimpsed at present, but are likely to come into focus in the future. The mechanism of selecting the initiation site for protein synthesis appears to follow a single formula. The translational machinery displays a certain flexibility that is exploited more frequently by viral than by cellular mRNAs. Although some of the parameters that determine efficiency have been identified, how efficiently a given mRNA will be translated cannot be predicted by summing the known parameters.

Repeat sequence families derived from mammalian tRNA genes

Short interspersed repetitive DNA sequences (SINEs) are the major component of dispersed repetitive DNA in all mammalian genomes. Most SINEs contain an intragenic RNA polymerase III promoter that initiates transcription at the 5' end of the repeated DNA sequence and which has been proposed to facilitate the transposition and amplification of these sequences by an RNA-intermediate mechanism. We have discovered several SINE families in the prosimian Galago crassicaudatus which have promoter regions similar to transfer RNA genes. To determine the relationship between Galago SINEs and mammalian tRNA genes, we have compared their sequences. Here, we demonstrate that the Galago monomer and type II SINE families are 68 and 62% homologous, respectively, with a human methionine tRNA gene. We have extended our analysis to include the rat identifier and mouse B2 families and show that their sequences are closely related to alanine and serine tRNA genes, respectively. Our observations suggest that many mammalian SINE families are amplified tRNA pseudogenes.

The accuracy of protein synthesis in reticulocyte and HeLa cell lysates

The accuracy of translation in protein synthesis is measured as the rate of misincorporation of a particular amino acid, different from that specified by an mRNA codon, into protein. The cowpea variant of tobacco mosaic virus, CcTMV, contains no cysteine or methionine in its coat protein. Translation in vitro of purified CcTMV coat protein mRNA by rabbit reticulocyte and HeLa cell lysates has been performed. The coat protein product was purified by immunoprecipitation with specific antisera, and separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The error rate was measured by comparing the incorporation of [35S]cysteine with incorporation of [3H]leucine, and the total CcTMV coat protein synthesized was calculated from its known leucine content. An error rate of (1-2) X 10(-3) cysteines/CcTMV coat protein was obtained with reticulocyte lysates. If errors were cysteine incorporation in place of arginine, this number is converted to 3 X 10(-4) cysteine/codon. If cysteine was incorporated anywhere in the polypeptide, the rate is 9 X 10(-6) cysteines/amino acid. The error frequencies with HeLa cell lysates were 6-fold higher. Paromomycin, a eukaryotic misreading antibiotic, increased error rates 10-fold in both lysates. These data compare well with in vivo measurements and suggest that some transformed cells may survive with higher mistranslation rates.

Translational activity of mRNA coding for cytoskeletal brain proteins in newborn and adult mice: a comparative study

Translational activity of mRNA coding for cytoskeletal brain proteins was used to determine the relative abundance of the mRNA in the brains of newborn and adult mice. mRNA was translated in a cell-free system containing rabbit reticulocyte factors. The products of translation were analyzed by two-dimensional gel electrophoresis and characterized by peptide map analysis. Comparison of the products of translation from newborn and from adult brain mRNA shows a 50% decrease in actin and tubulin from newborn to the adult stage. In contrast, the 70 kd neurofilament protein and glial fibrillary acidic protein show a twofold increase in the adult stage. The heat-shock protein HSP70 increases slightly (30%) whereas the brain isozyme of creatine kinase and the heat-shock protein HSP90 are three times as high in adult subjects as in newborns.

Molecular cloning of the complementary DNA for human tumor necrosis factor

Tumor necrosis factor (TNF) is a soluble protein that causes damage to tumor cells but has no effect on normal cells. Human TNF was purified to apparent homogeneity as a 17.3-kilodalton protein from HL-60 leukemia cells and showed cytotoxic and cytostatic activities against various human tumor cell lines. The amino acid sequence was determined for the amino terminal end of the purified protein, and oligodeoxyribonucleotide probes were synthesized on the basis of this sequence. Complementary DNA (cDNA) encoding human TNF was cloned from induced HL-60 messenger RNA and was confirmed by hybrid-selection assay, direct expression in COS-7 cells, and nucleotide sequence analysis. The human TNF cDNA is 1585 base pairs in length and encodes a protein of 233 amino acids. The mature protein begins at residue 77, leaving a long leader sequence of 76 amino acids. Expression of high levels of human TNF in Escherichia coli was accomplished under control of the bacteriophage lambda PL promoter and gene N ribosome binding site.

Insertion mutagenesis to increase secondary structure within the 5' noncoding region of a eukaryotic mRNA reduces translational efficiency

The thymidine kinase gene of herpes simplex virus 1 was mutated by inserting oligodeoxynucleotide linkers into the region of the gene corresponding to the 5' untranslated portion of the mRNA. These linkers, when transcribed into mRNA, might be expected to form hairpin loops and hence to increase the secondary structure of the 5' end of the mRNA. Thymidine kinase insertion derivatives were examined in vivo and in vitro to determine translational efficiency. For the in vivo studies, thymidine kinase insertion derivatives were transfected into thymidine kinase deficient L cells alone and together with a selectable dominant marker, or were assayed in the COS-1 transient expression system. For in vitro studies, thymidine kinase insertion derivatives were subcloned into pSP64. Capped transcripts were analyzed for their ability to bind ribosomes and translate in rabbit reticulocyte lysates and wheat-germ extracts. The results demonstrate that translation efficiency is decreased as the number of linkers is increased and support the view that excessive secondary structure at the 5' end of eukaryotic mRNA impedes translation.

Molecular cloning of potato spindle tuber viroid (PSTV) cDNA synthesized by enzymatic elongation of PSTV-specific DNA primers: a general strategy for viroid cloning

Different cDNAs were synthesized by primer extension from the RNA of the severe strain KF 440 of potato spindle tuber viroid (PSTV) with the aid of reverse transcriptase using three PSTV-specific DNA molecules as primers. The cDNAs were made double-stranded and cloned into plasmid pBR 322. Various overlapping subgenomic DNA fragments were prepared from these clones and recombined in two different ways. In both cases a PSTV DNA copy was obtained which represented the entire PSTV RNA genome. The sequence of the DNA of one of the resulting full-length clones was identical with the original PSTV isolate, whereas the other clone showed one nucleotide change. On the basis of these results the advantages and problems of different strategies for the molecular cloning of the circular viroid RNA genome are discussed.

Use of primer-restriction-end adapters in a novel cDNA cloning strategy

We introduce a class of synthetic oligonucleotides, referred to as primer-restriction-end (PRE) adapters, which are bifunctional, one end serving as a primer for a polymerase reaction, while the other end can be ligated to restriction endonuclease digested DNA. Use of such adapters forms the basis of a new method for inserting single-stranded cDNA into cloning vectors, which involves very few separate biochemical modifications of the cDNA and so is appropriate when extensive fractionation of cDNA is desired prior to cloning. This novel methodology is highly efficient in producing full-length cDNA cloned in a predictable orientation within vectors, as we demonstrate by constructing and analysing clones of immunoglobulin lambda light chain cDNA in Escherichia coli.

Regulation of mRNAs for three enzymes in the glial cell model C6 cell line

In the glial cell line C6, regulation of actinomycin D (Act-D)-sensitive translatable polysomal mRNAs of three key enzymes--glycerol phosphate dehydrogenase (GPDH; EC 1.1.1.8) and glutamine synthetase (GS) by glucocorticoids and lactate dehydrogenase (LDH; EC 1.1.1.27) by catecholamines--is described. Though the first two enzymes are hydrocortisone (HC)-inducible, the nature of their response to the hyperacetylating agent sodium butyrate is dramatically different. Furthermore the appearance of GPDH translatable poly(A)+ RNA in HC-induced cells is inhibited by the presence of cycloheximide (CHX), whereas the induction of GS is unaffected by CHX. These observations necessitate further probing into an existing model system to explain the varied mechanisms of induction of these two enzymes by a single inducer. In combination with the third enzyme whose induction by catecholamines is glial specific, we believe that the C6 cell represents the most appropriate cell line for molecular neurobiologists to study the mechanisms of hormone action in glia.