Conservation of the primary structure at the 3' end of 18S rRNA from eucaryotic cells

Characterization of the gene and an antigenic determinant of equine herpesvirus type-1 glycoprotein 14 with homology to gB-equivalent glycoproteins of other herpesviruses

The gene encoding glycoprotein 14 (gp14) of equine herpesvirus type 1 was sequenced. Nucleotide sequence analysis revealed a complete transcription unit composed of a CAT box, a TATA box, a ribosome-binding sequence, a polyadenylation signal and an open reading frame (ORF) of 2940 bp transcribed from left to right. The amino acid (aa) sequence deduced from this ORF corresponded to that of a protein with 979 aa and had the characteristic features of membrane gp including a 20-aa signal sequence at the N terminus, a 743-aa surface domain, a 40-aa membrane anchoring region, a 108-aa hydrophilic cytoplasmic domain at the C terminus and eleven potential sites for N-linked glycosylation. An unusual feature of this protein was an exceptionally long (66aa) sequence, with a preponderance of hydrophilic residues, preceding the hydrophobic signal core. An antigenic determinant recognized by an anti-gp14 monoclonal antibody was present in the N terminus of the postulated surface domain. Comparison of gp 14 with the gp of other herpesviruses indicated that gp14 was highly homologous to corresponding gp of pseudorabies (gII), bovine herpesvirus (gI), varicella-zoster virus (gII), as well as of herpes simplex virus, Epstein-Barr virus and human cytomegalovirus (gB).

GC balance in the internal transcribed spacers ITS 1 and ITS 2 of nuclear ribosomal RNA genes

The internal transcribed spacer (ITS) 1 and 2, the 5.8S rRNA gene, and adjacent 18S rRNA and 25S rRNA coding regions of two Cucurbitaceae (Cucurbita pepo, zucchini, ITS 1: 187 bp, and ITS 2: 252 bp in length, and Cucumis sativus, cucumber, ITS 1: 229 bp, and ITS 2: 245 bp in length) have been sequenced. The evolutionary pattern shown by the ITSs of these plants is different from that found in vertebrates. Deletions, insertions, and base substitutions have occurred in both spacers; however, it is obvious that some selection pressure is responsible for the preservation of stem-loop structures. The dissimilarity of the 5' region of ITS 2 found in higher plants has consequences for proposed models on U3 snRNA-ITS 2 interaction in higher eukaryotes. The two investigated Cucurbitaceae species show a G + C content of ITS 1 that nearly equals that of ITS 2. An analysis of the ITS sequences reveals that in 19 out of 20 organisms published, the G + C content of ITS 1 nearly equals that of ITS 2, although it ranges from 20% to 90% in different organisms (GC balance). Moreover, the balanced G + C content of the ITSs in a given species seems to be similar to that of so-called expansion segments (ESs) in the 25/28S rRNA coding region. Thus, ITSs show a phenomenon called molecular coevolution with respect to each other and to the ESs. In the ITSs of Cucurbitaceae the balanced G + C composition is at least partly achieved by C to T transitions, via deamination of 5-methylcytosine. Other mutational events must be taken into account. The appearance of this phenomenon is discussed in terms of functional constraints linked to the structures of these spacers.

Sequence and tissue distribution of a second protein of hepatic gap junctions, Cx26, as deduced from its cDNA

While a number of different gap junction proteins have now been identified, hepatic gap junctions are unique in being the first demonstrated case where two homologous, but distinct, proteins (28,000 and 21,000 Mr) are found within a single gap junctional plaque (Nicholson, B. J., R. Dermietzel, D. Teplow, O. Traub, K. Willecke, and J.-P. Revel. 1987. Nature [Lond.]. 329:732-734). The cDNA for the major 28,000-Mr component has been cloned (Paul, D. L. 1986. J. Cell Biol. 103:123-134) (Kumar, N. M., and N. B. Gilula. 1986. J. Cell Biol. 103:767-776) and, based on its deduced formula weight of 32,007, has been designated connexin 32 (or Cx32 as used here). We now report the selection and characterization of clones for the second 21,000-Mr protein using an oligonucleotide derived from the amino-terminal protein sequence. Together the cDNAs represent 2.4 kb of the single 2.5-kb message detected in Northern blots. An open reading frame of 678 bp coding for a protein with a calculated molecular mass of 26,453 D was identified. Overall sequence homology with Cx32 and Cx43 (64 and 51% amino acid identities, respectively) and a similar predicted tertiary structure confirm that this protein forms part of the connexin family and is consequently referred to as Cx26. Consistent with observations on Cx43 (Beyer, E. C., D. L. Paul, and D. A. Goodenough. 1987. J. Cell Biol. 105:2621-2629) the most marked divergence between Cx26 and other members of the family lies in the sequence of the cytoplasmic domains. The Cx26 gene is present as a single copy per haploid genome in rat and, based on Southern blots, appears to contain at least one intron outside the open reading frame. Northern blots indicate that Cx32 and Cx26 are typically coexpressed, messages for both having been identified in liver, kidney, intestine, lung, spleen, stomach, testes, and brain, but not heart and adult skeletal muscle. This raises the interesting prospect of having differential modes of regulating intercellular channels within a given tissue and, at least in the case of liver, a given cell.

Human adipocyte lipid-binding protein: purification of the protein and cloning of its complementary DNA

Human adipocyte lipid-binding protein (H-ALBP) was purified from normal subcutaneous adipose tissue to greater than 98% homogeneity, utilizing a combination of acid fractionation, gel filtration, covalent chromatography on activated thiol-Sepharose 4B, and anion-exchange chromatography. Human ALBP comprised about 1% of total cytosolic protein in human adipose tissue, had a relative molecular mass of about 15 kDa, and existed as a monomer in solution. The amino terminus of H-ALBP was blocked to sequencing. When a liposome ligand delivery assay was used, H-ALBP saturably bound oleic acid with about 1 mol of ligand bound per mole of protein. Additionally, H-ALBP saturably bound retinoic acid as determined by the quenching of intrinsic tryptophan fluorescence. A full-length H-ALBP cDNA has been cloned; the sequence predicts a 649-base mRNA comprised of a 62-base 5'-noncoding region containing an 18S ribosome-binding site, a single 396-base open-reading frame, and a 191-base 3'-noncoding region. Comparative sequence analysis indicated that the 132 amino acid H-ALBP is a member of a multigene family of intracellular lipid-binding proteins and contains the consensus substrate phosphorylation sequence for tyrosyl kinases.

Nucleotide sequence of the ononis yellow mosaic tymovirus genome

The nucleotide sequence of the genome of ononis yellow mosaic tymovirus (OYMV) has been determined. The genome is single-stranded RNA, 6211 nucleotides long, and has three main open reading frames (ORFs), two of them overlapping. The largest ORF (nucleotides 179-5509) encodes a polyprotein of 1776 amino acid residues that has sequence similarities with polymerases of other viruses with RNA genomes. The smaller overlapping ORF (nucleotides 172-1965) encodes a protein of 597 amino acids of unknown function. The third ORF located at the 3' end of the genome (nucleotides 5487-6065) is the virion protein gene, and it overlaps by 20 nucleotides the 3' terminus of the largest ORF. The organization of the OYMV genome, its sequence, and the sequences of the protein it encodes are clearly similar to those of two other tymoviruses, turnip yellow mosaic virus and eggplant mosaic virus. The 5' terminal noncoding region of the OYMV genome is much longer than the same region of other tymoviral genomes and includes a direct duplication of a sequence of 21-23 nucleotides.

Nucleotide sequence and cellular distribution of rat chromogranin B (secretogranin I) mRNA in the neuroendocrine system

The mRNA of rat secretory-vesicle protein chromogranin B is abundant in brain, adrenal medulla, and anterior pituitary. The primary translation product predicted from the cDNA sequence of this 2,337-nucleotide transcript corresponds to a hydrophilic 655-residue protein preceded by a signal peptide. Both termini of the mature 75-kD protein show extensive similarity to other chromogranins; the more variable internal region is characterized by glutamic acid clusters and numerous pairs of basic residues. In rodent brain, mRNA accumulation starts around embryonic days 13-14 and peaks by postnatal day 20. In situ hybridization in brain sections shows that the mRNA is enriched in the hippocampal formation, the endocrine hypothalamus, the olfactory system, and in anatomically distinct structures in the pons-medulla.

Translational efficiencies of polyomavirus late mRNA molecules that differ in the sequences of their 5' noncoding late leader exons

Mouse NIH 3T6 cells were coinfected with two strains of polyomavirus that differ only in the sequences of their 5' noncoding late leader exons. Polysomes were isolated at late times after infection and probed with oligonucleotides specific for each strain. Results indicate that the sequence of the late leader does not play a role in the translational efficiency of late polyomavirus messages.

An internal 5'-noncoding region required for translation of poliovirus RNA in vitro

A truncated poliovirus RNA that contains the entire 5'-noncoding region as well as some capsid protein-coding sequences was produced from cloned cDNA inserted into an SP6 transcription vector and subsequently was translated in a mixed rabbit reticulocyte-HeLa cell lysate. Deletions or modifications of regions of the 5'-noncoding sequences had significant effects upon the efficiency of translation. The presence of a 60-nucleotide sequence located at positions 567 to 627 appeared to be essential for active ribosome binding and translation of this uncapped RNA.

Analysis of cDNA encoding the hypoxanthine-guanine phosphoribosyltransferase (HGPRTase) of Schistosoma mansoni; a putative target for chemotherapy

Because of the lack of de novo purine biosynthesis, hypoxanthine-guanine phosphoribosyltransferase (HGPRTase) is a critical enzyme in the purine metabolic pathway of the human parasite, Schistosoma mansoni. Using a cDNA clone encoding mouse HGPRTase and subsequently a synthetic oligonucleotide derived from sequencing a clone of genomic DNA, two clones were isolated from an adult schistosome cDNA library. One clone is 1.374 Kilobases (Kb) long and has an open reading frame of 693 bases. The deduced 231 amino acid sequence has 47.9% identity in a 217 amino acid overlap with human HGPRTase. Northern blot analysis indicates that the full length of mRNA for the S. mansoni HGPRTase is 1.45-1.6 Kb. Analysis of the primary structures of the putative active site for human and parasite enzymes reveal specific differences which may eventually be exploitable in the design of drugs for the treatment of schistosomiasis.

Comparative sequence analysis of the 5' noncoding region of the enteroviruses and rhinoviruses

A comparative sequence analysis of the 5' noncoding region of a subgroup of the picornaviruses, including the polioviruses, coxsackie B3, and the human rhinoviruses, reveals the conservation of certain features despite the divergence of sequence. In this subgroup, for which nine complete sequences are available, two long stretches of sequence, two pyrimidine-rich regions, and 22 hairpins are conserved. Based on these results, similar secondary structures encompassing the entire 5' noncoding regions of these viruses are predicted. The fact that sequence divergence occurred only in a manner that allowed conservation of these structures implicates a biologically functional role for this region. The possible roles it may have in the picornavirus life cycle are discussed.

p1B15: a cDNA clone of the rat mRNA encoding cyclophilin

We present the complete nucleotide sequence of a cDNA encoding rat cyclophilin. The 743-nucleotide sequence contains a 42-nucleotide 5' noncoding region, a 492 nucleotide open reading frame corresponding to a translation product of 164 amino acids with a molecular weight of 17,874, and a 3' noncoding region of 209 nucleotides. Primer extension studies reveal the presence of one minor and two major transcription start sites. Southern blot analyses are consistent with as many as 20 copies of the cyclophilin gene and possible pseudogenes. Cyclophilin mRNA is expressed in virtually all types of tissues of rat and monkey and appears to have been highly conserved during mammalian evolution.

Nucleotide sequence determination and secondary structure of Xenopus U3 snRNA

Using a combination of RNA sequencing and construction of cDNA clones followed by DNA sequencing, we have determined the primary nucleotide sequence of U3 snRNA in Xenopus laevis and Xenopus borealis. This molecule has a length of 219 nucleotides. Alignment of the Xenopus sequences with U3 snRNA sequences from other organisms reveals three evolutionarily conserved blocks. We have probed the secondary structure of U3 snRNA in intact Xenopus laevis nuclei using single-strand specific chemical reagents; primer extension was used to map the positions of chemical modification. The three blocks of conserved sequences fall within single-stranded regions, and are therefore accessible for interaction with other molecules. Models of U3 snRNA function are discussed in light of these data.

SR alpha promoter: an efficient and versatile mammalian cDNA expression system composed of the simian virus 40 early promoter and the R-U5 segment of human T-cell leukemia virus type 1 long terminal repeat

We developed a novel promoter system, designated SR alpha, which is composed of the simian virus 40 (SV40) early promoter and the R segment and part of the U5 sequence (R-U5') of the long terminal repeat of human T-cell leukemia virus type 1. The R-U5' sequence stimulated chloramphenicol acetyltransferase (CAT) gene expression only when placed immediately downstream of the SV40 early promoter in the sense orientation. The SR alpha expression system was 1 or 2 orders of magnitude more active than the SV40 early promoter in a wide variety of cell types, including fibroblasts and lymphoid cells, and was capable of promoting a high level of expression of various lymphokine cDNAs. These features of the SR alpha promoter were incorporated into the pcD-cDNA expression cloning vector originally developed by Okayama and Berg.

Crosslinking of the anticodon of P site bound tRNA to C-1400 of E.coli 16S RNA does not require the participation of the 50S subunit

Crosslinking of the 5'-anticodon base of ribosomal P site bound AcVal-tRNA to residue C-1400 of 16S RNA or to its equivalent in 18S RNA has been shown to occur on 70S or 80S ribosomes of both prokaryotes and eukaryotes [Ciesiolka, J., Nurse, K., Klein, J. and Ofengand, J. (1985) Biochemistry 24, 3233-3239]. In the present work, we show that the crosslinking rate, crosslinking yield, and site of crosslinking are all unchanged when the 50S subunit is omitted. Therefore, all of the positional features of tRNA-ribosome complexes which allow crosslinking to occur are entirely contained in the 30S subunit. Blockage of reverse transcription by crosslink formation was used to determine the site of crosslinking. This analysis revealed that RNA modifications which do not directly block base-pairing ligands sometimes allow the modified base to be transcribed, leading to doublet band formation even when there is only a single crosslink site.

SR alpha promoter: an efficient and versatile mammalian cDNA expression system composed of the simian virus 40 early promoter and the R-U5 segment of human T-cell leukemia virus type 1 long terminal repeat

We developed a novel promoter system, designated SR alpha, which is composed of the simian virus 40 (SV40) early promoter and the R segment and part of the U5 sequence (R-U5') of the long terminal repeat of human T-cell leukemia virus type 1. The R-U5' sequence stimulated chloramphenicol acetyltransferase (CAT) gene expression only when placed immediately downstream of the SV40 early promoter in the sense orientation. The SR alpha expression system was 1 or 2 orders of magnitude more active than the SV40 early promoter in a wide variety of cell types, including fibroblasts and lymphoid cells, and was capable of promoting a high level of expression of various lymphokine cDNAs. These features of the SR alpha promoter were incorporated into the pcD-cDNA expression cloning vector originally developed by Okayama and Berg.

Signals determining translational start-site recognition in eukaryotes and their role in prediction of genetic reading frames

A special methionyl-tRNA (RNAi) is universally required to initiate translation. The conversation of this reactant throughout evolution, as well as its unusual decoding properties, suggested an alternate mechanism for tRNA-mRNA interactions at initiation. We have reported that the sequence of bases neighboring the start codons of many eubacterial genes are complementary not only to the 16S rRNA 3' end and to the anticodon of tRNAi, but, also, have the potential to base-pair the D, T or extended anticodon loops of this tRNAi. The coding properties of tRNAi and mutations that affect translation suggest that these signals may function. This hypothesis explains the observation that unusual triplets can start prokaryotic and mitochondrial genes and predicts the occurrence of other reading frames. Furthermore, it suggests a unifying model of chain initiation based on RNA-RNA contacts and displacements. Here we examine the start domain of 290 eukaryotic genes for their ability to base-pair the tRNAi loops and the 18S rRNA. We observe that both methionine start, and methionine coding regions have the potential to pair with the 18S rRNA, but that the nucleotide distribution about start codons strongly favoured such pairings over that near internal AUGs. The 5' extended anticodon of tRNAi is methylated, and was not represented in the mRNA with high frequency. However, the tetramer AUGg did occur with high frequency in the start domain. A modification of the tRNAi T loop also decreases its base-pairing potential. Interestingly, complementarity to the T loop did not occur with high frequency in the start sites. The early coding region, 10 to 34 nucleotides 3' to the initiator AUG, is complementary to the tRNAi D loop in many cases, while no such affinity is found near internal AUGs. The nucleotides around initiator AUGs were heavily biassed toward the sequence gccaccAUGgcg. No such tendency was noted around internal AUGs. Although the role of this sequence bias is unclear, the sequence gccaccAUGg has been shown by Kozak to promote initiation. Another distinguishing feature was a C-rich tract 7 to 34 nucleotides 5' to the initiator AUGs. Ability to pair with more than eight bases of the start consensus sequence, matching of 6 or 7 nucleotides to the D loop on the 3' side, an C-richness on the 5' side were used as criteria for distinguishing start AUGs.(ABSTRACT TRUNCATED AT 400 WORDS)

Trypanosome mRNAs have unusual "cap 4" structures acquired by addition of a spliced leader

A single capped oligonucleotide is released from Trypanosoma brucei poly(A)+ RNA upon digestion with RNase T2. This observation supports the hypothesis that all T. brucei mRNAs share a common leader sequence. Digestion of the T2-resistant species with nucleotide pyrophosphatase shows that the capping nucleotide is 7-methylguanosine 5'-monophosphate (pm7G). Additional characterization of the T2-resistant fragment indicates that modifications are present on the first four transcribed nucleotides; the 5' termini of T. brucei mRNAs can, therefore, be described as "cap 4" structures. Identical 5'-cap structures are found on the T. brucei spliced leader (SL) RNA; an observation compatible with the hypothesis that the small SL RNA acts as a donor of the SL for the mRNA. However, we find that within a population of purified SL RNAs are species that are capped but incompletely modified. The presence of these unmodified and partially modified species allowed us to analyze the 5' sequence of the SL RNA transcript. The results indicate that transcription begins four nucleotides upstream of the reported 5' end. Therefore, the T. brucei SL transcript is actually 39 rather than 35 nucleotides long. We have also analyzed the capped oligonucleotide of a distantly related Trypanosomatid, Leptomonas collosoma and find it to be identical to that of T. brucei. The potential significance of these results is discussed in light of observations of trypanosome gene expression.

Sequence and organization of southern bean mosaic virus genomic RNA

The genomic RNA sequence of the cowpea strain of southern bean mosaic virus (SBMV-C) has been determined. The genome is 4194 nucleotides in length and has four open reading frames. A 5' proximal open frame, from base 49 to base 603, corresponds to the length of the P4 proteins translated in cell-free extracts from full-length and smaller virion RNA. The largest open frame extends from base 570 to base 3437 and encodes the two largest proteins translated in cell-free extracts from full-length virion RNA. Segments of this open reading frame's predicted amino acid sequence resemble those of known viral RNA polymerases, ATP-binding proteins, and viral genome-linked proteins. A third open frame extends from base 1895 to base 2380 and has not been correlated with an in vitro translation product. The fourth open reading frame is located in the 3' terminal region of the genome extending from base 3217 to base 4053. This frame encodes the SBMV capsid protein which is translated from subgenomic, virion RNA.

Covalent cross-linking of AcVal-tRNA to Tetrahymena thermophila cytoplasmic ribosomes and two of its 17S rRNA mutants

Tetrahymena thermophila 80S ribosomes have been cross-linked to non-enzymatically bound AcVal-tRNA, presumably at the ribosomal P-site. Like the ribosomes from Escherichia coli, yeast, and Artemia salina, cross-linking is exclusively to C-1609, the equivalent of the E. coli C-1400 residue. Mutation of the RNA from G-1707 to A or from U-1711 to C which results in resistance to paromomycin or hygromycin, respectively, failed to affect the rate, yield, or site of cross-linking. The presence of the antibiotics during cross-linking also was without effect. It is concluded that at these two positions the base changes made do not interfere with the tertiary structure of the decoding site.

Effects of cDNA hybridization on translation of encephalomyocarditis virus RNA

Cell-free translation of the RNA of encephalomyocarditis virus was examined after hybridization of chemically synthesized cDNA fragments to different sites of the 5' noncoding region of the viral RNA. The following results were obtained. The binding of cDNA fragments to the first 41 nucleotides, to the poly(C) tract (between nucleotides 149 and 263), and to the sequence between nucleotides 309 and 338 did not affect translation of the viral RNA; the binding of cDNA fragments to the sequence between nucleotides 420 and 449 caused a slight inhibition; and the binding of fragments to eight different sites between nucleotides 450 and the initiator AUG codon (nucleotide 834) caused high degrees of inhibition. The results suggest that the first part of the 5' untranslated region, at least to nucleotide 338, may not be required for encephalomyocarditis viral RNA translation; however, the region near nucleotide 450 is important for translation of the viral RNA. The possibility that initiation occurs at an internal site is discussed.

Sites of action of two ribosomal RNA methylases responsible for resistance to aminoglycosides

Methylation of either of two residues (G-1405 or A-1408) within bacterial 16 S ribosomal RNA results in high level resistance to specific combinations of aminoglycoside antibiotics. The product of a gene that originated in Micromonospora purpurea (an actinomycete that produces gentamicin) gives resistance to kanamycin plus gentamicin by converting residue G-1405 to 7-methylguanosine. Resistance to kanamycin plus apramycin results from conversion of residue A-1408 to 1-methyladenosine catalysed by the product of a gene from Streptomyces tenjimariensis.

Characterisation of the 5'-leader sequence of tobacco mosaic virus RNA as a general enhancer of translation in vitro

Uncapped messenger RNAs (mRNAs) encoding calf preprochymosin, chicken prelysozyme, or Escherichia coli beta-glucuronidase (GUS) were synthesized in vitro, with or without a 5'-terminal 67-nucleotide sequence (omega') derived from the untranslated 5'-leader (omega) of tobacco mosaic virus (TMV) RNA. Messenger RNAs were translated in vitro, in messenger-dependent systems derived from rabbit reticulocytes (MDL), wheat-germ (WG) or E. coli (EC). The omega' sequence enhanced expression of each mRNA in almost every translation system. While MDL was the least responsive to omega', this sequence proved particularly efficient in permitting translation of the eukaryotic mRNAs in EC, despite the absence of a consensus Shine-Dalgarno sequence in either the mRNAs or omega'. The local context of the initiation codon (AUG) in two GUS mRNA constructs did not influence the relative enhancement caused by the omega' sequence. These findings extend the utility of omega' as a general enhancer of translation for both prokaryotic and eukaryotic mRNAs in either 80S- or 70S-ribosome-based systems.

The nucleotide sequence of the gB glycoprotein gene of HSV-2 and comparison with the corresponding gene of HSV-1

The nucleotide sequence of the gB glycoprotein gene of HSV-2 has been determined and compared with the homologous gene of HSV-1. The two genes are specified by the same total number of codons (904); eight additional codons of the HSV-1 gene are found within the signal sequence, and eight additional codons of the HSV-2 gene are found at three different sites in the gene. The signal cleavage, membrane-spanning, and eight potential N-linked oligosaccharide sites, as well as 5'- and 3'-regulatory signals are largely conserved. The overall amino acid homology is 85%; least conserved are the N- and C-terminal regions of the protein. Secondary structure plots were determined for the two proteins, and the structures were compared with each other and with alterations in structure due to several mutations in the HSV-1 gB gene for which sequence analysis is available. The high homology in primary and secondary structure suggests a conserved, essential function for the gene.

Sequence organisation and transcriptional regulation of the mouse elastase II and trypsin genes

Elastase II and trypsin mRNAs were cloned in form of their cDNAs from pancreas of strain A/J mice, and their complete nucleotide sequences were determined. The elastase II mRNA is 912 nucleotides long and encodes a protein of 271 amino acids. The cloned trypsin mRNA species is 814 nucleotides long and encodes a protein of 246 amino acids. The elastase II gene, which exists as a single copy in the haploid mouse genome, measures 11.2 kb from cap to poly(A) site and is interrupted by at least seven introns. Between 5 and 10 trypsin genes exist in the mouse genome. Five different trypsin genes, two of which are closely linked in a tail-to-tail manner, were studied in detail. They vary in size between 3.4 and 4.0kb, and all are interrupted by four introns. DNA sequence comparison of the elastase II, trypsin and Amy-2a alpha-amylase genes reveals a conserved 13 nucleotide motif in their 5'-flanking regions. The differential accumulation of the elastase II and trypsin mRNAs in the cytoplasm of the acinar pancreatic cell is regulated predominantly at the transcriptional level.

The 66 kDa component of eukaryotic initiation factor 3 interacts with globin mRNA and 18 S rRNA in preinitiation complexes

The 66 kDa protein present in a complex with globin mRNA and 18 S rRNA [(1984) Eur. J. Biochem. 143, 27-33] has been reincorporated into functional eukaryotic initiation factor 3 (eIF-3) under conditions of protein synthesis. Additionally, two-dimensional polyacrylamide gel electrophoresis has been used to demonstrate the identity of the 66 kDa protein with the 66 kDa subunit of eIF-3.

Ovine beta-lactoglobulin messenger RNA: nucleotide sequence and mRNA levels during functional differentiation of the mammary gland

The nucleotide sequence of ovine beta-lactoglobulin mRNA has been determined by chemical sequencing of two cDNA recombinant plasmids and primer extension products. Ovine beta-lactoglobulin mRNA consists of a 540 nucleotide coding region, flanked by 39 nucleotide 5' and 206 nucleotide 3' non-coding regions including a 20 nucleotide poly A tail. The deduced 180 amino acid sequence of pre-beta-lactoglobulin is in agreement with the previously published amino acid sequence of signal peptide and mature protein. Northern blot analysis of poly A+ RNAs from the lactating mammary glands of porcine, rabbit and rat species, allowed us to identify a homologous RNA to beta-lactoglobulin mRNA solely in the porcine species. We also detected a mRNA transcript of a size similar to that of beta-lactoglobulin mRNA in hepatic poly A+ RNA from female rat liver treated by estrogens. Furthermore, we have examined the levels of beta-lactoglobulin mRNA during the functional differentiation of the mammary gland and after hormonal stimulation. During the last third of pregnancy, the expression of beta-lactoglobulin gene is significantly more elevated than that of alpha s1- or beta-casein whose mRNA levels were found to change very slightly during this period. Both beta-lactoglobulin and casein mRNAs showed a rapid response and a wide range of change in response to cortisol treatment. However, there was a significant difference in the rate at which these processes occurred, suggesting that beta-lactoglobulin gene expression is regulated independently of the casein genes.

Amino acid sequence of mammalian elongation factor 2 deduced from the cDNA sequence: homology with GTP-binding proteins

Complementary DNA clones, pHEW1 and pRE2, coding for hamster and rat polypeptide chain elongation factor 2 (EF-2), respectively, were isolated and sequenced. It was shown that the cDNA insert in pHEW1 contains a 2574-base-pair open reading frame coding for an 857-amino acid polypeptide with Mr 95,192, excluding the initiation methionine. Comparative studies of sequence homology among EF-2 and several GTP-binding proteins show that five regions in the amino-terminal position of EF-2, corresponding to about 160 amino acids, show homology with GTP-binding proteins, including protein synthesis elongation and initiation factors, mammalian ras proteins, and transducin. The carboxyl-terminal half of EF-2 contains several regions that have 34-75% homology with bacterial elongation factor G. These results suggest that the amino-terminal region of EF-2 participates in the GTP-binding and GTPase activity whereas the carboxyl-terminal region interacts with ribosomes. Finally, the sequence provides direct evidence that diphthamide (2-[3-carboxy-amido-3-(trimethylammonio)propyl]histidine), the site of ADP-ribosylation by diphtheria toxin, is produced by post-translational modification of a histidine residue in the primary translational product.

Identification of the locations of the methyl groups in 18 S ribosomal RNA from Xenopus laevis and man

The 18 S ribosomal RNA from a variety of vertebrate species contains some 40 to 47 methyl groups. The majority of these are 2'-O-ribose substituents; the remaining few are on bases. Several lines of evidence have permitted the identification of the precise locations of the methyl groups in the primary structure of 18 S ribosomal RNA of Xenopus laevis and man. Digestion of RNA with T1 ribonuclease, followed by analysis of the methylated oligonucleotides yielded data on sequences immediately surrounding the methyl groups. Preparative hybridization of X. laevis 18 S ribosomal RNA restriction fragments of ribosomal DNA, followed by fingerprinting analysis on RNA recovered from the hybrids, allowed each methylated oligonucleotide to be mapped to a specific region within 18 S ribosomal RNA. The data on RNA oligonucleotides were correlated with Xenopus ribosomal DNA sequence data in the regions defined by the mapping experiments to identify the precise locations of most of the methyl groups in the X. laevis 18 S RNA sequence. The remaining uncertainties in Xenopus were solved with the aid of data from ribonuclease A fingerprints and, in a few instances, relevant oligonucleotide or sequence data from other laboratories. The locations of most of the methyl groups in human 18 S ribosomal RNA were deduced from the high degree of correspondence between methylated oligonucleotides from human and X. laevis 18 S RNA, together with knowledge of the human 18 S ribosomal DNA sequence. The remaining methylation sites in human 18 S RNA were located with assistance from relevant published comparative data. In the aligned sequences, human and other mammalian 18 S RNA are methylated at all the same positions as in X. laevis, and there are seven additional 2'-O-methylation sites in mammalian 18 S RNA. Further features of the methyl group distribution are briefly reviewed.

Structure of the Eip28/29 gene, an ecdysone-inducible gene from Drosophila

The EIPs 28 and 29 are a family of polypeptides identified originally by their ecdysone inducibility in Drosophila cell lines. At least two family members, 28III and 29III, appear to be primary translation products. Here we describe a unique Eip28/29 gene that must encode both primary products. The Eip28/29 gene is unique because the cloned genomic DNA hybridizes to both EIP 28 and 29 messenger RNAs under stringent conditions, but does not anneal detectably to other genomic sequences even under mild conditions. Furthermore the diverse products of this gene are not alleles because flies homozygous for the chromosomal region (71CD) containing the Eip28/29 gene produce mRNAs that translate to yield all the EIPs 28 and 29. We report here the sequence of a 2855-nucleotide region encompassing the Eip28/29 gene. By comparisons with complementary DNA sequences and by nuclease protection experiments we have derived a complete structure for the Eip28/29 transcription unit. The primary transcript is 2146 nucleotides long and is processed by the removal of three introns to yield the predominant mature transcript in tissue culture cells (979 nucleotides). This transcript probably corresponds to the 28III mRNA. Neither the start of the transcription unit nor the structure of the predominant transcript is affected by the hormone ecdysone. The genomic sequence reveals a series of heptanucleotide and octanucleotide repeats of unknown function that fall at about 50-nucleotide intervals within the first 150 nucleotides upstream from the transcription unit. In addition this sequence, when combined with previously published data, suggests that the consensus cap site sequence in Drosophila may be extended to include 13 nucleotides centered on the heptanucleotide core previously recognized by Snyder et al. (1982).

Direct purification of polyadenylated RNAs from isolated polysome fractions

We report a simplified and improved method for obtaining polyadenylated RNAs (poly(A) RNAs) from polysome fractions. Isolated polysomes were subjected directly to poly(U)-Sephadex column chromatography without conventional purification of polysomal RNAs by phenol extraction followed by ethanol precipitation. The yield of poly(A) RNAs by this direct purification method was about twice that obtained by the conventional method. When the two poly(A) RNA preparations were used in two-dimensional polyacrylamide gel electrophoretic analysis of cell-free translation products and cDNA synthesis, biological activity of the directly purified poly(A) RNA was equal to or even better than that of conventionally purified poly(A) RNA.

Novel serine proteases encoded by two cytotoxic T lymphocyte-specific genes

Genes that are expressed exclusively in cytotoxic T cells should encode proteins that are essential for target cell lysis in cell-mediated immune responses. The sequences of two cytotoxic T lymphocyte-specific complementary DNA's (cDNA's) suggest that the two genes encode serine proteases. A full-length cDNA corresponding to one of the genes was isolated and sequenced. The predicted protein resembles serine proteases in that it includes all the residues that form the catalytic triad of the active site of serine proteases. Moreover, it has sequence characteristics thought to occur only in rat mast cell protease type II. These results are in accord with the view that a protease cascade plays a key role in cytotoxic T-cell activation.

Eukaryotic mRNA 5'-leader sequences have dual regions of complementarity to the 3'-terminus of 18s rRNA

We have used a microcomputer program to test eukaryotic mRNA 5'-leader sequences for complementarity to the 3'-terminus of 18S rRNA. No mismatched bases, bulge loops, or viral mRNA's were utilized. At least one-fourth of the more than 200 mRNA's studied were found to have two distinct regions of complementarity which resulted in an ability to bind to two separate rRNA regions (GAAGG and UUUGG). The analysis of 60 mRNAs with these dual sites resulted in a consensus structure that was a mean distance of 11.75 bases 5' from the initiator AUG and had an average predicted interstrand binding strength of delta G = -13.40 kcal. These characteristics compare favorably to those observed for the prokaryotic 16S rRNA-mRNA Shine and Dalgarno bond.

Rapid chemical probing of conformation in 16 S ribosomal RNA and 30 S ribosomal subunits using primer extension

We have investigated in detail the higher-order structure of 16 S ribosomal RNA, both in its naked form and in 30 S ribosomal subunits. Each base in the 16 S rRNA chain has been probed using kethoxal (which reacts with guanine at N1 and N2), dimethylsulfate (which reacts with adenine at N1 and cytosine at N3) and 1-cyclohexyl-3-(2-morpholinoethyl)-carbodiimide metho-p-toluenesulfonate (which reacts with uracil at N3 and guanine at N1). The sites of reaction were identified by primer extension with reverse transcriptase using synthetic oligodeoxynucleotide primers. These results provide a detailed and rigorous experimental test of a model for 16 S rRNA secondary structure, which was derived mainly from comparative sequence analysis. Our data also provide information relevant to tertiary and quaternary structure of 16 S rRNA. Data obtained with naked 16 S rRNA show reasonably close agreement with the proposed model, and data obtained with 30 S subunits show nearly complete agreement. Apart from an apparent overall "tightening" of the structure (in which many weakly reactive bases become unreactive), assembly of the proteins with 16 S rRNA to form 30 S subunits brings about numerous local structural rearrangements, resulting in specific enhancements as well as protections. In many instances, the ribosomal proteins appear to "tune" the 16 S rRNA structure to bring it into accordance with the phylogenetically predicted model, even though the RNA on its own often seems to prefer a different structure in certain regions of the molecule. Extensive protection of conserved, unpaired adenines upon formation of 30 S subunits suggests that they play a special role in the assembly process, possibly providing signals for protein recognition.

Structural features of the 5' noncoding region of the rabbit globin messenger RNAs engaged in translation

Accessible sites in the 5' noncoding region of the rabbit alpha- and beta-globin mRNAs were identified and compared in deproteinized RNA and in the mRNAs engaged in translation in the reticulocyte lysate. Preparations of RNA and lysate were subjected to limited nuclease digestion by RNase T1 and Neurospora endonuclease, and the cleavage sites were analyzed by a nuclease S1 mapping procedure. The free alpha-globin mRNA contained few nuclease-sensitive sites and its initiation codon AUG was masked. The free beta-globin mRNA contained a larger number of accessible sites and its AUG was highly exposed. The distribution of sensitive sites differed considerably in the lysate. In both mRNA species, a site near the 5' terminus became the one most accessible to Neurospora endonuclease. Also the accessibility of the AUG in beta-globin mRNA decreased considerably. The distribution of accessible sites in the lysate was the same when the mRNAs were undergoing rapid initiation and when initiation became limited after prolonged incubation. Inhibition of initiation by the cap analogue 7-methylguanosine 5'-triphosphate was accompanied by increased sensitivity of some of the sites in both mRNA species. One of the accessible sites in each mRNA species had a sequence complementary to the 3'-terminal portion of the 18S ribosomal RNA.

Nonepidermal members of the keratin multigene family: cDNA sequences and in situ localization of the mRNAs

A keratin set which consists of a type I 47kd and a type II 57kd protein occurs as a major constituent of the keratin patterns of various internal stratified epithelia of the mouse. We have isolated specific cDNA clones of the two complementary keratin subunits from a cDNA library constructed with polyA+RNA of mouse tongue epithelium and present the complete nucleotide and deduced amino acid sequences of the 57kd protein and about 75% of the corresponding data of the 47kd protein. The comparison of the sequence data with those of known epidermal keratin mRNAs coding for the two types of keratin proteins reveals a fundamentally identical and type-specific organization of the mRNAs into both highly conserved and variable domains. In order to avoid cross-reactions with other members of the keratin multigene family, appropriately taylored 35S-labeled cDNA probes comprising the low and non-homologous 3' coding and noncoding domains of the mRNAs were used for in situ hybridization to tissue sections. The localization and distribution of the corresponding transcripts indicates a strongly compartmentalized keratin expression in mouse tongue epithelium.