Deletion of the Escherichia coli pseudouridine synthase gene truB blocks formation of pseudouridine 55 in tRNA in vivo, does not affect exponential growth, but confers a strong selective disadvantage in competition with wild-type cells

Previous work from this laboratory (Nurse et al., RNA, 1995, 1:102-112) established that TruB, a pseudouridine (psi) synthase from Escherichia coli, was able to make psi55 in tRNA transcripts but not in transcripts of full-length or fragmented 16S or 23S ribosomal RNAs. By deletion of the truB gene, we now show that TruB is the only protein in E. coli able to make psi55 in vivo. Lack of TruB and psi55 did not affect the exponential growth rate but did confer a strong selective disadvantage on the mutant when it was competed against wild-type. The negative selection did not appear to be acting at either the exponential or stationary phase. Transformation with a plasmid vector conferring carbenicillin resistance and growth in carbenicillin markedly increased the selective disadvantage, as did growth at 42 degrees C, and both together were approximately additive such that three cycles of competitive growth sufficed to reduce the mutant strain to approximately 0.2% of its original value. The most striking finding was that all growth effects could be reversed by transformation with a plasmid carrying a truB gene coding for a D48C mutation in TruB. Direct analysis showed that this mutant did not make psi55 under the conditions of the competition experiment. Therefore, the growth defect due to the lack of TruB must be due to the lack of some other function of the protein, possibly an RNA chaperone activity, but not to the absence of psi55.

Oxalate oxidases and differentiating surface structure in wheat: germins

Oxalate oxidases (OXOs) have been found to be concentrated in the surface tissues of wheat embryos and grains: germin is concentrated in root and leaf sheaths that surround germinated embryos; pseudogermin (OXO-psi) is concentrated in the epidermis and bracts that 'encircle' mature grains. Most strikingly, the epidermal accumulation of OXO-psi was found to presage the transition of a delicate 'skin', similar to the fragile epidermis of human skin, into the tough shell (the miller's 'beeswing') that is typical of mature wheat grains. A narrow range of oxalate concentration (1--2 mM) in the hydrated tissues of major crop cereals (barley, maize, oat, rice, rye and wheat) contrasted with wide variations in their OXO expression, e.g. cold-tolerant and cold-sensitive varieties of maize have similar oxalate contents but the former was found to contain approx. 20-fold more germin than did the latter. Well-known OXOs in sorghum, a minor cereal, and beet, a dicotyledon, were found to have little antigenic relatedness to the germins, but the beet enzyme did share some of the unique stability properties that are peculiar to the germin-like OXOs that are found only in the major crop cereals. Their concentration in surface structures of domesticated wheat suggests a biochemical role for germin-like OXOs: programmed cell death in surface tissues might be a constitutive as well as an adaptive form of differentiation that helps to produce refractory barriers against tissue invasion by predators. Incidental to the principal investigation, and using an OXO assay (oxalate-dependent release of CO(2)) that did not rely on detecting H(2)O(2), which is often fully degraded in cell extracts, it was found that OXO activity in soluble extracts of wheat was manifested only in standard solution assays if the extract was pretreated in a variety of ways, which included preincubation with pepsin or highly substituted glucuronogalactoarabinoxylans (cell-wall polysaccharides).

Isolation and properties of Escherichia coli 23S-RNA pseudouridine 1911, 1915, 1917 synthase (RluD)

All nine pseudouridine (psi) residues in Escherichia coli 23S RNA are in or very near the peptidyl transfer centre (PTC) of the ribosome. Five psi synthases catalyze synthesis of these nine psi's. Deletion of the gene for one psi synthase, RluD, which directs synthesis of three closely clustered psi's in the decoding site of the PTC, has a profound negative impact on cell growth. We describe the isolation, without amplification from a cloned coding element, of the triple-site modifying enzyme, RluD, the N-terminal sequence of which has been used to clone and express the corresponding gene, rluD. Unlike "expressed" RluD, which so far has not been shown to modify one (1911) of the three closely clustered sites (1911, 1915, 1917), "natural" RluD modifies all three sites; and unlike another pai synthase, RluA, natural RluD has greatly expanded modifying activity at low Mg concentrations. These properties of the expressed and natural forms of RluD are discussed.

Functional effect of deletion and mutation of the Escherichia coli ribosomal RNA and tRNA pseudouridine synthase RluA

The Escherichia coli gene rluA, coding for the pseudouridine synthase RluA that forms 23 S rRNA pseudouridine 746 and tRNA pseudouridine 32, was deleted in strains MG1655 and BL21/DE3. The rluA deletion mutant failed to form either 23 S RNA pseudouridine 746 or tRNA pseudouridine 32. Replacement of rluA in trans on a rescue plasmid restored both pseudouridines. Therefore, RluA is the sole protein responsible for the in vivo formation of 23 S RNA pseudouridine 746 and tRNA pseudouridine 32. Plasmid rescue of both rluA- strains using an rluA gene carrying asparagine or threonine replacements for the highly conserved aspartate 64 demonstrated that neither mutant could form 23 S RNA pseudouridine 746 or tRNA pseudouridine 32 in vivo, showing that this conserved aspartate is essential for enzyme-catalyzed formation of both pseudouridines. In vitro assays using overexpressed wild-type and mutant synthases confirmed that only the wild-type protein was active despite the overexpression of wild-type and mutant synthases in approximately equal amounts. There was no difference in exponential growth rate between wild-type and MG1655(rluA-) either in rich or minimal medium at 24, 37, or 42 degrees C, but when both strains were grown together, a strong selection against the deletion strain was observed.

16S ribosomal RNA pseudouridine synthase RsuA of Escherichia coli: deletion, mutation of the conserved Asp102 residue, and sequence comparison among all other pseudouridine synthases

The gene for RsuA, the pseudouridine synthase that converts U516 to pseudouridine in 16S ribosomal RNA of Escherichia coli, has been deleted in strains MG1655 and BL21/DE3. Deletion of this gene resulted in the specific loss of pseudouridine516 in both cell lines, and replacement of the gene in trans on a plasmid restored the pseudouridine. Therefore, rsuA is the only gene in E. coli with the ability to produce a protein capable of forming pseudouridine516. There was no effect on the growth rate of rsuA- MG1655 either in rich or minimal medium at either 24, 37, or 42 degrees C. Plasmid rescue of the BL21/DE3 rsuA- strain using pET15b containing an rsuA gene with aspartate102 replaced by asparagine or threonine demonstrated that neither mutant was active in vivo. This result supports a role for this aspartate, located in a unique GRLD sequence in this gene, at the catalytic center of the synthase. Induction of wild-type and the two mutant synthases in strain BL21/DE3 from genes in pET15b yielded a strong overexpression of all three proteins in approximately equal amounts showing that the mutations did not affect production of the protein in vivo and thus that the lack of activity was not due to a failure to produce a gene product. Aspartate102 is found in a conserved motif present in many pseudouridine synthases. The conservation and distribution of this motif in nature was assessed.

Cloning and characterization of the 23S RNA pseudouridine 2633 synthase from Bacillus subtilis

A Bacillus subtilis ORF, ypul, 41% homologous to rsuA, the gene for the synthase which forms pseudouridine 516 in Escherichia coli 16S rRNA, was cloned and the protein expressed and affinity-purified by the His tag procedure. Reactions with E. coli 16S and 23S rRNA transcripts were performed in vitro. The protein did not form pseudouridine 516 as expected but did produce pseudouridine 552 in 16S rRNA and pseudouridines 1199, 2605, and 2833 in 23S rRNA. Of these, only pseudouridine 2605 is found naturally in either E. coli or B. subtilis rRNA. Kinetic experiments confirmed that pseudouridine 2605 was the primary target. Comparison of the four pseudouridine sites yielded a consensus recognition sequence for the synthase. This consensus sequence was not present at any other site in either E. coli or B. subtilis 16S or 23S RNA. We propose that YpuL is the B. subtilis pseudouridine 2633 (2605 in E. coli) synthase. Since the closest gene sequence homologue in E. coli is yciL, we suggest that its gene product is the corresponding E. coli pseudouridine 2605 synthase.

The pseudouridine residues of ribosomal RNA

Pseudouridine (psi), the most common single modified nucleoside in ribosomal RNA, has been positioned in the small subunit (SSU) and large subunit (LSU) RNAs of a number of representative species. Most of the information has been obtained by application of a rapid primed reverse transcriptase sequencing technique. The locations of these psi residues have been compared. Many sites for psi are the same among species, but others are distinct. In general, the percentage psi in multicellular eukaryotes is greater than in prokaryotes. In LSU RNA, the psi residues are strongly clustered in three domains, all of which are near or connected to the peptidyl transferase center. There is no apparent clustering of psi in SSU RNA. The psi sites in LSU RNA overlap those for the methylated nucleosides, but this is not the case in SSU RNA. There are 265 psi sites known to nucleotide resolution, of which 246 are in defined secondary structures, and 112 of these are in nonidentical structural contexts. All 246 psi sites can be classified into five structural types. Two Escherichia coli psi synthases have been cloned and characterized, one for psi 516 in SSU RNA and one for psi 746 in LSU RNA. The psi 746 synthase recognizes free RNA, but the psi 516 enzyme requires an intermediate RNP particle. Possible functional roles for psi in the ribosome are discussed.

Participation of acetylpseudouridine in the synthesis of a peptide bond in vitro

Uracil, uridine, and pseudouridine were acetylated by refluxing in acetic anhydride, and the products of acetylation were incubated with a synthetic peptide (1-21) that corresponds to the N-terminal 21 amino acid residues of human myelin basic protein. Peptide bond formation, at the N alpha terminus in peptide 1-21, was obtained with acetyluracil and acetylpseudouridine, but not with acetyluridine. Transfer of an acetyl group from acetyluracil and acetylpseudouridine depended on acetylation in the N-heterocycle. X-ray crystallographic analysis definitively established N-1 as the site of acetylation in acetyluracil. Mass spectrometry of the acetylation products showed that one acetyl group was transferred to peptide 1-21, in water, by either acetyluracil or acetylpseudouridine at pH approximately 6. Release of the acetyl group by acylaminopeptidase regenerated peptide 1-21 (mass spectrometry) and automated sequencing (for five cycles) of the regenerated (deacetylated) peptide demonstrated that the N terminus was intact. The findings are discussed in the context of a possible role for pseudouridine in ribosome-catalyzed peptidyltransfer, with particular reference being made to similarities between the possible mechanism of acyl transfer by acetyluracil/pseudouridine and the mechanism of carboxyl transfer by carboxylbiotin in acetyl CoA carboxylase. The possibility that idiosyncratic appearance of a wide range of acyl substituents in myelin basic protein could be related to a peculiar involvement of ribosomal pseudouridine is mentioned.

Purification, cloning, and properties of the 16S RNA pseudouridine 516 synthase from Escherichia coli

Pseudouridine (psi) is commonly found in both small and large subunit ribosomal RNAs of prokaryotes and eukaryotes. In Escherichia coli small subunit RNA, there is only one psi, at position 516, in a region of the RNA known to be involved in codon recognition [Bakin et al. (1994) Nucleic Acids Res. 22, 3681-3684]. To assess the function of this single psi residue, the enzyme catalyzing its formation was purified and cloned. The enzyme contains 231 amino acids and has a calculated molecular mass of 25,836 Da. It converts U516 in E. coli 16S RNA transcripts into psi but does not modify any other position in this RNA. It does not react with free unmodified 16S RNA at all, and only poorly with 30S particles containing unmodified RNA. The preferred substrate is an RNA fragment from residues 1 to 678 which has been complexed with 30S ribosomal proteins. The yield varied from 0.6 to 1.0 mol of psi/mol of RNA, depending on the preparation. Free RNA(1-678) was inactive, as was RNA(1-526) and the RNP particle made from it. 23S RNA and tRNAVal transcripts were also inactive. These results suggest that psi formation in vivo occurs at an intermediate stage of 30S assembly. The gene is located at 47.1 min immediately 5' to, and oriented in the same direction as, the bicyclomycin resistance gene. The gene was cloned behind a (His)6 leader for affinity purification. Virtually all of the overexpressed protein was found in inclusion bodies but could be purified to homogeneity on a Ni2+(-) containing resin. Over 200 mg of pure protein could be obtained from a liter of cell culture. Amino acid sequence comparison revealed the existence of a gene in Bacillus subtilis with a similar sequence, and psi sequence analysis established that B. subtilis has the equivalent of psi 516 in its small subunit rRNA. On the other hand, no common sequence motifs could be detected among this enzyme and the two tRNA psi synthases which have been cloned up to now.

A dual-specificity pseudouridine synthase: an Escherichia coli synthase purified and cloned on the basis of its specificity for psi 746 in 23S RNA is also specific for psi 32 in tRNA(phe)

An Escherichia coli pseudouridine (psi) synthase, which forms both psi 746 in E. coli 23S ribosomal RNA and psi 32 in tRNA(Phe), has been isolated and cloned. The enzyme contains 219 amino acids and has a calculated MW of 24,432 Da. Amino acid sequence comparison with the three other psi synthases that have been cloned to date, two for tRNA and one for 16S RNA, did not reveal any common sequence motifs, despite the catalysis of a common reaction. The gene was cloned behind a (His)6 leader for affinity purification. Upon overexpression, most of the enzyme remained soluble in the cell cytoplasm and could be purified to homogeneity on a Ni(2+)-containing resin. The enzyme reacted with both full-length 23S RNA or a fragment from residues 1-847, forming 1 mol psi/mol RNA at position 746, a normal site for psi. The enzyme has no dependence on Mg2+. The same yield was obtained in 1 mM EDTA as in 10 mM Mg2+, and the rate was faster in EDTA than in Mg2+. Full-length 16S RNA or fragments 1-526 or 1-678, as well as tRNA(Val) transcripts, were not modified in either EDTA or Mg2+. tRNA(Phe) transcripts, however, were modified with a yield of 1 mol psi/mol transcript at a rate in EDTA like that of 23S RNA. Sequencing showed all of the psi to be at position 32, a normal site for psi in this tRNA. Both 23S rRNA psi 746 and tRNA psi 32 occur in single-stranded segments of the same sequence, psi UGAAAA, closed by a stem. Therefore, this synthase may require for recognition only a short stretch of primary sequence 3' to the site of pseudouridylation. This is the first example of a dual-specificity modifying enzyme for RNA, that is, one which is specific for a single site in one RNA, and equally site-specific in a second class of RNA. The essentiality of these psi residues can now be assessed by disruption of the synthase gene.

Purification, cloning, and properties of the tRNA psi 55 synthase from Escherichia coli

tRNA pseudouridine 55 (psi 55) synthase, the enzyme that is specific for the conversion of U55 to psi 55 in the m5U psi CG loop in most tRNAs, has been purified from Escherichia coli and cloned. On SDS gels, a single polypeptide chain with a mass of 39.7 kDa was found. The gene is a previously described open reading frame, p35, located at 68.86 min on the E. coli chromosome between the infB and rpsO genes. The proposed name for this gene is truB. There is very little protein sequence homology between the truB gene product and the hisT (truA) product, which forms psi in the anticodon arm of tRNAs. However, there was high homology with a fragment of a Bacillus subtilis gene that may produce the analogous enzyme in that species. The cloned gene was fused to a 5'-leader coding for a (His)6 tract, and the protein was overexpressed > 400-fold in E. coli. The recombinant protein was purified to homogeneity in one step from a crude cell extract by affinity chromatography using a Ni(2+)-containing matrix. The SDS mass of the recombinant protein was 41.5 kDa, whereas that calculated from the gene was 37.3. The recombinant protein was specific for U55 in tRNA transcripts and reacted neither at other sites for psi in such transcripts nor with transcripts of 16S or 23S ribosomal RNA or subfragments. The enzyme did not require either a renatured RNA structure or Mg2+, and prior formation of m5U was not required. Stoichiometric formation of psi occurred with no requirement for an external source of energy, indicating that psi synthesis is thermodynamically favored.

Pseudouridine and O2'-methylated nucleosides. Significance of their selective occurrence in rRNA domains that function in ribosome-catalyzed synthesis of the peptide bonds in proteins

Pseudouridine (5-ribosyluracil, psi) was the first of a host of modified nucleoside constituents detected in cellular RNA and it remains the most abundant, being broadly distributed in the RNA of archaebacteria, eubacteria and eukaryotes. Like some other modifications, psi is particularly abundant in more complex organisms, reaching 2-3% of the total nucleoside constituents in tRNA, snRNA and rRNA of multicellular plants and animals. Like all other modified nucleosides, psi arises by site-specific, enzymically catalyzed modification of a nucleoside residue in an RNA molecule. Unlike all other modified nucleosides, psi arises by isomerisation (not substitution) of a classical nucleoside, uridine (1-ribosyluracil). There have been suggestions that key processes such as ribosome assembly and peptidyl transfer may rely, more than is generally appreciated, on RNA modifications such as O2'-methylation and pseudouridylation, respectively. However, a persuasive case for the view that secondary modifications are of primary importance in ribosome function has not been convincingly made. Accordingly, we think it is timely to broaden what is generally meant by the 'catalytic properties of rRNA', and to ask, to what extent do modifications contribute to in vivo rates of ribosome assembly and ribosomal peptide-bond synthesis? The first part of this article sets forth the evidence that there is a conspicuous association between modified nucleosides and cellular RNAs that participate in group-transfer reactions. The second part reviews evidence in support of the view that the functions of psi and other modified nucleosides are likely of central importance for understanding the dynamics and stereostructural modeling at functionally significant sites in the ribosome.

Clustering of pseudouridine residues around the peptidyltransferase center of yeast cytoplasmic and mitochondrial ribosomes

Analysis of the high molecular weight RNAs of the larger ribosomal subunit of Saccharomyces cerevisiae cytoplasm and mitochondria by a new method [Bakin, A., & Ofengand, J. (1993) Biochemistry 32, 9754-9762] has for the first time located all of the pseudouridine residues present in these two RNAs. Thirty pseudouridines were found in the cytoplasmic RNA, and one was found in the mitochondrial RNA. The 30 cytoplasmic RNA pseudouridines were clustered in three regions of the RNA known to be at or near the peptidyltransferase center. The single pseudouridine in yeast mitochondrial rRNA at position 2819 was also located at the peptidyltransferase center. The localization of pseudouridines at or near the peptidyltransferase center in both cytoplasmic and mitochondrial ribosomes implies a functional role for pseudouridine in peptide bond formation. A correlation was shown to exist between the locations of the pseudouridines determined in this work and the positions of the methylated nucleotides (both 2'-OCH3 and base-methylated) determined previously by others. In addition, this work has tentatively identified the locations of two previously unknown ribothymidine residues, at positions 955 and 2920 in the cytoplasmic rRNA.

Oxalate, germin, and the extracellular matrix of higher plants

The article assembles and elaborates evidence which indicates that an 'old' enzyme, oxalate oxidase, and an even 'older' substrate, calcium oxalate, have significant and previously uncontemplated roles in the biochemistry of the extracellular matrix (ECM) of higher plants. These possibilities emerged by chance, but not really by chance, when computerized comparisons of amino acid sequences inevitably led to the discovery that germin, long known to be a protein marker of the onset of growth in germinating wheat, and later known to be an ECM protein, is an oxalate oxidase [J. Biol. Chem. 268, 12239-12242 (1993)]. Dissolution of calcium oxalate, and germin-induced degradation of the resulting soluble oxalate, can release Ca2+ and H2O2, both of which are known to have central roles in the biochemistry of the ECM in higher plants. It is therefore timely to survey the implications of the recent finding that germin is an oxalate oxidase in the context of how oxalate may participate not only in the biochemistry of the ECM, but in the development of higher plants. The findings about oxalate, as a source of H2O2, are a complement to Varner's contemporaneous advocacy of a central role for H2O2 in the development, differentiation, vascularization and signaling processes of higher plants.

Germin, a protein marker of early plant development, is an oxalate oxidase

Germin is a homopentameric glycoprotein, the synthesis of which coincides with the onset of growth in germinating wheat embryos. There have been detailed studies of germin structure, biosynthesis, homology with other proteins, and of its value as a marker of wheat development. Germin isoforms associated with the apoplast have been speculated to have a role in embryo hydration during maturation and germination. Antigenically related isoforms of germin are present during germination in all of the economically important cereals studied, and the amounts of germin-like proteins and coding elements have been found to undergo conspicuous change when salt-tolerant higher plants are subjected to salt stress. In this report, we describe how circumstantial evidence arising from unrelated studies of barley oxalate oxidase and its coding elements have led to definitive evidence that the germin isoform made during wheat germination is an oxalate oxidase. Establishment of links between oxalate degradation, cereal germination, and salt tolerance has significant implications for a broad range of studies related to development and adaptation in higher plants. Roles for germin in cell wall biochemistry and tissue remodeling are discussed, with special emphasis on the generation of hydrogen peroxide during germin-induced oxidation of oxalate.

Germin isoforms are discrete temporal markers of wheat development. Pseudogermin is a uniquely thermostable water-soluble oligomeric protein in ungerminated embryos and like germin in germinated embryos, it is incorporated into cell walls

Nascent synthesis and accumulation of germin and its mRNA mark the onset of renewed growth when wheat embryos are germinated in water. Germin is a water-soluble, pepsin-resistant protein that is not found in immature embryos, or in mature embryos before their germination. An antiserum was raised by injecting rabbits with germin that was freed of other proteins by pepsinization and gel filtration. The antiserum has been used to detect, in extracts of mature embryos from dry, ungerminated wheat grains, a protein that is antigenically related to germin. The antigenically related protein has been named pseudogermin. Pseudogermin accumulates, maximally, between 20-25-days postanthesis, then declines appreciably in amount by 30-days postanthesis, in soluble extracts of immature embryos from several wheat varieties. The antiserum was also used to identify germin and pseudogermin among the proteins extracted from cell walls and to bind immunogold to cell walls preparatory to visualizing freeze-cleaved embryos by scanning electron microscopy. Wall-associated germin accounts for about 40% of the total germin in germinating wheat embryos. Appearance of germin in the apoplast is the most conspicuous germination-related change in the distribution of cell-wall proteins. It seems that germin may act at the level of the apoplast and that pseudogermin may subsume the role of germin at low water potentials during embryogenesis. The N-terminal eicosapeptide sequences in germin and pseudogermin are very similar but SDS/PAGE analysis detects discrete differences between the mobilities of their constituent monomers as well as gross differences between the stabilities of the parent oligomers. Like germin, pseudogermin is a water-soluble, pepsin-resistant protein, but pseudogermin has unprecedented disulphide-independent thermostability properties that have never been previously reported for a water-soluble oligomeric protein. Polysaccharides that co-purify with otherwise pure specimens of germin (and pseudogermin) have been isolated for analysis and shown to be highly substituted glucuronogalactoarabinoxylans. The possible biological significance of selective and tenacious association between germin and glucuronogalactoarabinoxylans is discussed in relation to cell expansion during embryogenic and germinative development of wheat, as are some peculiarities of amino-acid sequence that suggest a possible relation between germin and a proton-specific ion pump: gastric ATPase.

Wheat Ec metallothionein genes. Like mammalian Zn2+ metallothionein genes, wheat Zn2+ metallothionein genes are conspicuously expressed during embryogenesis

A cDNA library was prepared from the bulk mRNA of mature wheat embryos and screened with mixed 32P-labeled oligonucleotide probes that encoded parts of the partial amino-acid sequence for the Zn-containing Ec protein. Each DNA insert in 11 positives from a screen of 10(5) plaques encoded a 5' untranslated and a 3' untranslated region, in addition to an open reading frame (of 81 amino acids) which, in every case, corresponded to at least 56 of the 59 amino acids in the partial polypeptide sequence previously determined for the Ec protein. The three different mRNA sequences encoded in the cDNA probably correspond to single-copy genes in the A, B and D genomes of hexaploid wheat. A wheat genomic library was screened with 32P-labeled cDNA and gave a single positive in a screen of 5 x 10(5) plaques. A 3.1-kb genomic fragment (gf-3.1) was sequenced and a cap site for the encoded mRNA was determined by primer extension. The gf-3.1 sequence encodes an intronless mRNA for the Ec protein and contains appreciable amounts of 5' and 3' flanking sequences. In addition to a putative TATA box, two inverted-repeat sequences and one direct-repeat sequence, the 5' flank in gf-3.1 contains a sequence similar to the abscisic-acid-responsive element in other higher-plant genes but does not contain sequences similar to the metal-responsive elements in animal metallothionein genes. Consistent with these findings, RNA blotting shows that accumulation of Ec mRNA is abundant in immature embryos, undetectable in germinated embryos and can be induced by adding abscisic acid, but not by adding Zn2+ to the medium in which mature wheat embryos are germinated. The findings suggest that the wheat Ec metallothionein genes, like mammalian liver metallothionein genes, are conspicuously expressed during embryogenesis.

Pseudouridine in the large-subunit (23 S-like) ribosomal RNA. The site of peptidyl transfer in the ribosome?

On evolutionary grounds, it has been advocated for more than 40 years that RNA generally, and more recently rRNA in particular, may participate, catalytically, in protein biosynthesis. A specific molecular mechanism has never been proposed. We suggest here that the N-1 position(s) in one or more of the approximately 4 pseudouridine (omega) residues in E. coli 23 S rRNA catalyzes transfer of the aminoacyl moiety from teh 3'-terminus of peptidyl tRNA in the P site to aminoacyl tRNA in the A site of the ribosome. Evidence that supports the proposal in the case of E. coli ribosomes, and relevant information pertaining to eukaryotic ribosomes, is summarized. Essential features of the evidence are that (i) the N-1 position in 1-acetylthymine (a direct analogue of 1-acetylpseudouridine) has an especially high potential for acyl-group transfer, comparable to that found for N-acetylimidazole (Spector, L.B. and Keller, E.B. (1958) J. Biol. Chem. 232, 185-192), (ii) most of the omega residues in prokaryotic 23 S rRNA are confined to the peptidyl transferase center in E. coli ribosomes, and (iii) Um-Gm-omega, the most densely modified sequence in eukaryotic 26 S rRNA, is universally conserved at a fixed site in the putative peptidyl transferase center of all eukaryotic ribosomes.

Cellular desiccation and hydration: developmentally regulated proteins, and the maturation and germination of seed embryos

Little more than a decade ago, 2-dimensional mapping of proteins and biochemical study of their allied coding elements (mRNA and DNA) were first used to probe possible changes in the embryo during seed germination. Because specification was of primary importance, our attention was initially directed toward the characterization of individual proteins and coding elements which, in preliminary surveys of the germinating wheat embryo, were found to be conspicuously subject to developmental regulation. Three of the proteins have become subjects of comprehensive investigations in this and other laboratories: the Em protein, the Ec protein, and germin. The Em and Ec proteins are encoded by the conserved mRNA 'stored' in the mature embryos of dry, field-ripened seeds but germin is encoded by the nascent mRNA formed after mature embryos are germinated in water. The Ec protein is the only bona fide Zn metallothionein yet found in higher plants. Studies of their biology and molecular biology suggest that the Em protein has a role in hormone-mediated (abscisic acid) cellular desiccation and that germin has a role in hormone-mediated (auxin) cellular hydration. It is projected that further studies of the Em protein may help elucidate the molecular basis for a loss of dessication tolerance during germination, and that further studies of germin may help elucidate the molecular basis of plant cell enlargement.

Homologies between members of the germin gene family in hexaploid wheat and similarities between these wheat germins and certain Physarum spherulins

By screening approximately 10(6) plaques in a wheat DNA library with a "full-length" germin cDNA probe, two genomic clones were detected. When digested with EcoRI, one clone yielded a 2.8-kilobase pair fragment (gf-2.8) and the other yielded a 3.8-kilobase pair fragment (gf-3.8). By nucleotide sequencing, each of gf-2.8 and gf-3.8 was found to encode a complete sequence for germin and germin mRNA, and to contain appreciable amounts of 5'- and 3'-flanking sequences. The "cap" site in gf-2.8 was determined by primer extension and the corresponding site in gf-3.8 was deduced by analogy. The mRNA coding sequences in gf-2.8 and gf-3.8 are intronless and 87% homologous with one another. The 5'-flanking regions in gf-2.8 and gf-3.8 contain recognizable sites of what are probably cis-acting elements but there is otherwise little if any significant similarity between them. In addition to putative TATA and CAAT boxes in the 5'-flanking regions of gf-2.8 and gf-3.8, there are AT-rich inverted-repeats, GC boxes, long purine-rich sequences, two 19-base pair direct-repeat sequences in gf-2.8, and a remarkably long (200-base pair) inverted-repeat sequence (approximately 90% homology) in gf-3.8. An 8% difference between the mature-protein coding regions in gf-2.8 and gf-3.8 is reflected by a corresponding 7% difference between the corresponding 201-residue proteins. Most significantly, the same 8% difference between the mature-protein coding regions in gf-2.8 and gf-3.8 is allied with no change whatever in a central part (61-151) of the encoded polypeptide sequences. It seems likely that this central, strongly conserved core in the germins is of first importance in the biochemical involvements of the proteins. When an equivalence is assumed between like amino acids, the gf-2.8 and gf-3.8 germins show significant (approximately 44%) similarity to spherulins 1a and 1b of Physarum polycephalum, a similarity that increases to approximately 50% in the conserved core of germin. Near the middle (87-96) of the conserved core in the germins is a rare PH(I/T)HPRATEI decapeptide sequence which is shared by spherulins (1a and 1b) and germins (gf-2.8 and gf-3.8). These similarities are discussed in the context of evidence which can be interpreted to suggest that the biochemistry of germins and spherulins is involved with cellular, perhaps cell-wall responses to desiccation, hydration, and osmotic stress.(ABSTRACT TRUNCATED AT 400 WORDS)

Covalently bonded and adventitious glycans in germin

Germin was previously shown to contain covalently bonded and adventitious glycans. The object of the present investigation was to characterize the two types of glycan. The presence of N- but not O-glycans in germin is indicated by the biosynthesis of altered forms, including an unglycosylated form of germin when wheat embryos are germinated in the presence of tunicamycin. After treating the doublet of germin pentamers (G and G') from normally germinated embryos with beta-N-acetylglucosaminidase, G is converted to a form that co-migrates with G' during electrophoresis in sodium dodecyl sulfate-polyacrylamide, but G' is unaffected. This suggests that the N-glycans in G contain antennary N-acetylglucosamine but that those in G' do not. This conclusion has been confirmed and elaborated by doubly labeling G and G' in vivo with [3H]glucosamine and [35S]methionine, and by characterizing sugar-labeled glycopeptides from G and G' by gel filtration, before and after their degradation by exoglycosidases. In the context of proven structures for the complex N-glycans in other plant glycoproteins, the findings, when combined with monosaccharide analyses of G and G', permit plausible speculation about the structure of the single N-glycan that is likely present in each G monomer (GlcNAc2(Man)2(Man-Xyl)(GlcNAc)(GlcNAc-Fuc] and G' monomer ((Man)2(Man-Xyl)(GlcNAc)(GlcNAc-Fuc)). The adventitious glycans, which can be removed by phenolic extraction of germin, have a composition similar to that expected for the characteristic hemicelluloses and pectins in monocot cell walls. The possible significance of this finding is discussed in relation to our continuing efforts to define the biochemical involvements of germin. In allied studies, affinity of its N-linked glycans for concanavalin A has been used to concentrate small amounts of germin from large volumes of wheat extract and to fractionate germin from tunicamycin-treated and normally germinated wheat embryos.

Polypeptide structure of germin as deduced from cDNA sequencing

Synthesis of a relatively rare glycoprotein (germin) signals the onset of growth in germinating wheat embryos. Germin mRNA (1075 nucleotide residues) has an 85-residue 5'-untranslated sequence, a 69-residue sequence that can encode a 23-residue signal-peptide sequence, a 603-residue sequence that can encode a 201-residue mature-protein sequence, and a 318-residue 3'-untranslated sequence that begins with a UAA-terminator codon, ends with a 63-residue polyadenylate tract, and has three polyadenylation (and other, related) signals (AAUAAN etc.). One polyadenylation signal is just 9 nucleotides from the polyadenylation site, the shortest stretch of nucleotides yet found between polyadenylation signal and site in any animal or plant mRNA. The mature-protein coding sequence in germin mRNA contains an unusually high proportion (87%) of G + C in the third positions of its codons. The amino acid sequence of germin does not have extensive internal homologies or repetitions, and it is not characterized by regions of unusually high charge density, as is nucleoplasmin, another water-soluble homopentameric protein with otherwise closely related structural properties. Germin does, however, contain a stretch of 34 uncharged amino acid residues and these may possibly mediate its homopentameric structure and its remarkable resistance to enzymic proteolysis. In view of a possible association of germin with cellular membranes, the most interesting relatedness of the germin sequence to the sequences of other proteins is an 80% homology between a decapeptide sequence in mature germin and a decapeptide sequence in Escherichia coli glycerol-3-phosphate acyltransferase. The relation of germin-gene structure to overall gene regulation during early plant growth is discussed.

Signal resistance of a soluble protein to enzymic proteolysis. An unorthodox approach to the isolation and purification of germin, a rare growth-related protein

Onset of growth in germinating wheat embryos is marked by the conspicuous synthesis of germin, a soluble homopentameric protein. Germin is unusually stable in reducing environments containing sodium dodecyl sulfate, but the polymeric form is converted to a protomer (ca. 26 kdaltons) by brief heat treatment. In respect to these physical properties, germin is similar to nucleoplasmin, the putative nucleosome-assembly factor in Xenopus oocytes. To expand the comparison, we treated germin with gastric pepsin in the expectation that pepsin-catalyzed hydrolysis of germin might generate a series of fragments of the kind derived by pepsin digestion of nucleoplasmin. To our surprise, germin was refractory under conditions used to degrade nucleoplasmin. Further study has shown that germin exhibits a measure of stability toward the action of broad-specificity proteases which is unprecedented for a soluble protein. In this report, we document the remarkable resistance of this growth-related protein to enzymic proteolysis and project how this property may make it possible to isolate and purify an otherwise intractably rare, but "interesting" protein.

A novel protein programmed by the mRNA conserved in dry wheat embryos. The principal site of cysteine incorporation during early germination

If bulk mRNA from dry wheat embryos (wheat germ) is used to direct cell-free incorporation of [35S]cysteine into proteins, a striking proportion of the total radioactivity is channeled into a single protein. During early postimbibition development, when protein synthesis is directed by the mRNA conserved in dry embryos, incorporation of cysteine is preponderantly (20-25%) directed into synthesis of this one protein: the 'early' cysteine-labeled protein (Ec). When conserved mRNA from the dry embryos has been fully degraded, as when cellular or cell-free protein synthesis is directed by the mRNA in germinated embryos, synthesis of Ec is not detected. Reliable detection of Ec requires prior alkylation of wheat embryo proteins, and it was especially interesting to find that when wheat embryo proteins are alkylated by iodo[14C]acetamide, two proteins co-dominate the distribution of radioalkylated products in dodecylsulphate/polyacrylamide gels: Ec and wheat germ agglutinin. Using co-electrophoresis with the isotopically labeled protein to detect a dye-staining counterpart, Ec has been purified by combined cation-exchange and gel-filtration chromatography of alkylated wheat germ proteins. The purified protein can be recovered in milligram quantity (5-10 mg/100 g wheat germ) and compositional analysis shows that it is unusually rich in cysteine (approx. 15%) and glycine (approx. 17%), as is wheat germ agglutinin.

Synthesis and turnover of proteins and mRNA in germinating wheat embryos

The most prominent methionine-labeled protein made when cell-free systems are programmed with bulk mRNA from dry wheat embryos has been identified with what may be the most abundant protein in dry wheat embryos. The protein has been brought to purity and has a distinctive amino acid composition, Gly and Glx accounting for almost 40% of the total amino acids. Designated E because of its conspicuous association with early inhibition of dry wheat embryos, the protein and its mRNA are abundant during the "early" phase (0--1 h) of postimbibition development, and easily detected during "lag" phase (1--5 h), but they are almost totally degraded soon after entry into the "growth" phase of development, by about 10 h postimbibition. The most prominent methionine-labeled protein peculiar to the cell-free translational capacity of bulk mRNA from "growth" phase embryos is not detected as a product of in vivo synthesis. Its electrophoretic properties and its time course of emergence, after 5 h postimbibition development, suggest that this major product of cell-free synthesis may be an in vitro counterpart to a prominent methionine-labeled protein made only in vivo, by "growth" phase embryos. Designated G because of its conspicuous association with "growth" phase development, the cell-free product does not comigrate with any prominent dye-stained band in electrophoretic distributions of wheat proteins. The suspected cellular counterpart to G, also, does not comigrate with a prominent dye-stained wheat protein during electrophoresis, and although found in particulate as well as soluble fractions of wheat embryo homogenates it is not concentrated in either nuclei or mitochondria, as isolated.

"Cap" sequences in poly(A)-rich RNA from dry wheat embryos

Although template-active RNA in dry seeds and embryos has attracted widespread interest, there have been no published reports about 5'-terminal "capping" sequences in such RNA. Boro[3H]hydride labeling of periodate-oxidized termini and high performance liquid chromatography of cap oligonucleotides have been used to compare terminal sequences in poly(A)-rich RNA from dry and germinating embryos. As is the case in germinating embryos, poly(A)-rich RNA from dry embryos contains only "type 0" cap sequences, i.e., m7G(5')ppp(5')N, in which m7G is the 7-methylguanosine cap and N is any of the classical ribonucleosides: adenosine (A), guanosine (G), cytidine (C),a nd uridine (U). Striking differences between the cell-free translational capacities of bulk messenger RNA (mRNA) populations from dry and germinating embryos are not reflected in signal differences in their proportions of "type 0" cap structures: in general, there is approximately 40% m7G(5')ppp(5')A, with roughly equivalent amounts of m7G(5')ppp(5')G and m7G(5')ppp(5')C accounting for most of the remaining sequences. The findings with mRNA from dry plant embryos serve to emphasize interesting differences between patterns of methylation in the capped and uncapped RNA molecules in higher plants and animals; the differences have not been previously noted in the literature and are the subject of brief comment in this paper.

Structural integrity of DNA and translational integrity of ribosomes in nuclease-treated cell-free protein synthesizing systems prepared from wheat germ and rabbit reticulocytes

After treatment at a microsomal nuclease concentration too low to reduce the endogenous amino acid-incorporating activity of freshly prepared reticulocyte lysate, there is little, if any, intact 26 S RNA left in the ribosomes of either wheat germ or rabbit reticulocyte cell-free protein synthesizing extracts. The primary scissions, probably at highly exposed sites in the rRNA of plant and animal ribosomes, produce two fragments which remain complexed until thermal denaturation reveals "hidden breaks." Molecular weights of the fragments are approximately 0.5 x 10(6) and 0.8 x 10(6) in the case of wheat, and 0.4 x 10(6) and 1.3 x 10(6) in the case of rabbit. There is little perceptible degradation of 5 S, 5.8 S, and 18 S rRNA, or of tRNA in the same extracts. Even though limited degradation of 26 S rRNA by a reticulocyte nuclease has been reported to severely impair the translational mechanism in reticulocyte ribosomes, micrococcal nuclease-induced degradation of rRNA, whether limited or extensive, does not seriously impair the ability of reticulocyte lysates to discriminate, by selective polypeptide synthesis, between complex populations of cellular mRNA. In an allied study, it is shown that under conditions well suited to recovery of the 5.8 S/26 S rRNA complex, with its naturally occurring hidden break, 5 S/18 S rRNA complexing is not detectable in the RNA or metabolizing embryos, nor in the RNA from untreated or nuclease-treated protein synthesizing extracts from wheat and rabbit. The significance of this finding is briefly elaborated in relation to the suggestion that 5 S rRNA may interact with the M2(6)A-m2(6)A hairpin near the 3'-end of 18 S rRNA.

Comparative study of levels of secondary processing in bulk mRNA from dry and germinating wheat embryos

There has been no previous study of levels of secondary processing in the template-active RNA of dry seeds and embryos. Such information is needed to evaluate the role of transcription in changing the cell-free translational capacity of bulk RNA during early imbibition of water by dry wheat embryos [J. Biol. Chem. 255, 5969-5970 (1980)]. Although it probably contains a higher proportion of "hidden breaks' than bulk mRNA from imbibing embryos, bulk mRNA in dry wheat embryos is also "capped' by 7-methylguanosine at 5' termini, devoid of unmethylated "caps', methylated internally (N6-methyladenosine) and polyadenylated at 3' termini. In contrast to other developing systems, there is no evidence that there are signal changes in levels of secondary processing in the bulk mRNA populations which support change in cell-free translational capacity of RNA 1-5 h postimbibition of dry wheat embryos. Change in the pattern of protein synthesis 5-24 h postimbibition also takes place without signal changes in levels of secondary processing in template-active RNA. The analytical data are evaluated and discussed in terms of difficulties allied with comparative analyses of poly(A)-rich RNA from dry and imbibing embryos, the former being refractory to, and the latter being most easily analyzed by, labeling in vivo.

Relation of protein synthesis in imbibing wheat embryos to the cell-free translational capacities of bulk mRNA from dry and imbibing embryos

Dry wheat embryos were allowed to imbibe water in the presence or absence of an inhibitor of mRNA synthesis (alpha-amanitin). At each of a series of times after the onset of imbibition, newly synthesized polypeptides were labeled, isolated, and compared with those made by cell-free translation of RNA prepared from the same embryos. In the absence of alpha-amanitin, characteristic time-dependent changes in the relative proportions of many polypeptides in the electrophoretic distributions of proteins synthesized in imbibing wheat embryos could be correlated with parallel changes in the cell-free translational capacity of bulk mRNA from the same embryos. These changes were virtually eliminated when alpha-amanitin was present in the imbibing medium. The findings are consistent with the possibility that transcription of new mRNA, which begins with the onset of imbibition, is responsible for change in the electrophoretic distributions of nascent polypeptides between 40 min and 5 h postimbibition of dry wheat embryos (Cuming, A. C. & Lane, B. G (1979) Eur. J. Biochem. 99, 217-224). Allied with the principal investigation, a useful modification has been developed in order to obtain an improved field of resolution (encompassing a range of Mr values between less than 5 X 10(5) and greater than 200 X 10(3), without using a gradient in sodium dodecyl sulfate/polyacrylamide gel.

Wheat embryo ribonucleates. XIV. Mass isolation of mRNA from wheat germ and comparison of its translational capacity with that of mRNA from imbibing wheat embryos

Commercially milled wheat germ is shown to be a convenient source material for facile recovery of mass (milligram) quantities of highly purified poly(A)-rich RNA. This poly(A)-rich RNA is efficiently translated in a nuclease-treated extract of rabbit reticulocytes. By sucrose density gradient fractionation of bulk poly(A)-rich RNA from wheat germ, it has been possible to show that there is a direct relationship between the molecular weights of the polypeptide products of cell-free synthesis and the molecular weights of the wheat mRNA molecules which program their synthesis. As assessed by SDS -- polyacrylamide gel electrophoresis, the same array of polypeptides is synthesized when nuclease-treated reticulocyte extract is programmed by poly(A)-rich RNA from either commercially supplied or laboratory-prepared wheat embryos. Significantly, there are gross quantitative if not qualitative differences between the translational capacities of poly(A)-rich RNA from dry and imbibing wheat embryos, and the possible importance of these differences for interpreting a changing pattern of polypeptide synthesis in imbibing wheat embryos is the subject of a brief discussion.

Protein synthesis in imbibing wheat embryos

Polypeptides synthesized by imbibing wheat embryos have been compared with those made by cell-free extracts programmed with bulk poly(A)-rich RNA from dry wheat embryos. Newly synthesized polypeptides, labeled with [35S]methionine, were resolved by one-dimensional and two-dimensional electrophoresis and then records of the separations were prepared by fluorography. When programmed by bulk poly(A)-rich RNA from dry wheat embryos, a nuclease-treated rabbit reticulocyte lysate synthesizes an array of polypeptides which is broadly similar to that formed when a wheat germ extract is programmed with the same RNA. Polypeptides made in both homologous and heterologous cell-free systems, under the direction of bulk poly(A)-rich RNA from dry wheat embryos, are broadly similar to those formed during early (0--40 min) imbibition of dry wheat embryos. As imbibition progresses beyond 40 min, there are profound changes in the one-dimensional and two-dimensional electrophoretic distributions of newly made polypeptides present in the 23 000 x g supernatant fraction of cell-free homogenates; characteristically, low-molecular-weight and basic polypeptides comprise a diminishing proportion of the total polypeptides as imbibition progresses beyond 40 min. Ribosomal proteins are conspicuous among the proteins formed during early imbibition and especially prominent among the products formed when homologous cell-free polypeptide synthesis is programmed by bulk poly(A)-rich RNA from dry wheat embryos.

Wheat embryo ribonucleates. XIII. Methyl-substituted nucleoside constituents and 5'-terminal dinucleotide sequences in bulk poly(AR)-rich RNA from imbibing wheat embryos

(1) N6-Methyladenosine, not previously detected as a component of plant mRNA, is shown to be present in the poly(A)-rich RNA which is isotopically labeled when wheat embryos imbibe water in a medium which contains [methyl-3H]methionine.(2) N6-Methyladenosine and 7-methylguanosine 'caps' can constitute more than 85% of the radioactivity when specimens of poly(A)-rich [methyl-3H]RNA are freed of most of the radioactivity contributed by contaminating rRNA, N6-methyladenosine accounting for 75–80% and 7-methylguanosine accounting for 20–25% of this radioactivity.(3) There are three principal 5′-terminal dinucleotide sequences (type 0 'cap' structures) in the poly(A)-rich RNA from imbibing wheat embryos: m7GpppA, m7GpppG, and m7GpppC.(4) The proportional distribution of radioactivity among the 5′-terminal dinucleotide sequences varies with the time of labeling of the imbibing wheat embryos (30 min and 24 h), m7GpppA being the most 'rapidly labeled' sequence and m7GpppC being the most 'slowly labeled' sequence.(5) Poly(A)-rich mRNA from imbibing wheat embryos is distinct from the corresponding RNA from any other organism yet studied in terms of its component methyl-substituted nucleosides and 5′-terminal dinucleotide sequences. The possible significance of these differences, as well as signal similarities between the poly(A)-rich mRNA of imbibing wheat embryos and other organisms, are subjects of discussion.

Wheat embryo ribonucleates. XII. Formal characterization of terminal and penultimate nucleoside residues at the 5'-ends of "capped" RNA from imbibing wheat embryos

(1) N2,N2,7-Trimethylguanosine, not previously detected as a component of plant RNA, is shown to be present in the RNA which is isotopically labelled when dry wheat embryos imbibe water in a medium that contains[methyl-3H]methionine. (2) N2,N2,7-Trimethylguanosine and 7-methylguanosine are released as part of "capped" oligonucleotides when the isotopically labelled RNA from imbibing wheat embryos is subjected to hydrolysis by RNase T2. (3) By way of contrast with the "capped" RNA of animal cells, 5'-terminal "cap" structures (m7Gppp- and m32,2,7 Gppp-) in the "capped" RNA from the higher plant organism are not bonded to pneultimate O2'-methylnucleoside constituents. (4) In an allied study, it has been found that recovery of poly (A)-rich RNA from dry wheat embryos depends on the inclusion of sodium dodecyl sulphate (SDS) in phosphate-buffered (pH 6.8) phenolic emulsions. By way of contrast, recovery of poly (A)-rich RNA from dry wheat embryos does not depend on the inclusion of SDS in Tris (hydroxymethyl) aminomethane buffered (pH 9.0) phenolic emulsions.

Wheat embryo ribonucleates XI. Conserved mRNA in dry wheat embryos and its relation to protein synthesis during early inhibition

It has been found that bulk poly(A)-rich RNA from dry wheat embryos is broadly heterodisperse when examined by polyacrylamide gel electrophoresis. The poly(A)-rich RNA from dry wheat embryos has been translated in a cell-free protein-synthesizing system from the same commerically supplied, roller-milled wheat embryos. Compatiable with the electrophoretic heterodispersity observed for poly(A)-rich RNA, the radioactive products of its cell-free translation, when examined by sodium dodecyl sulphate polyacrylamide gel electrophoresis, have mobilities that are broadly coincident with the many dye-stained (nonradioactive) proteins present in wheat extracts. With due allowance for the limitations of the cell-free system, which is known to translate, selectively, lower molecular-weight species of mRNA, it has been concluded that the conserved poly(A)-rich mRNA in dry wheat embryos probably has the translational capacity required to account for the highly eclectic protein synthesis that we have observed during early (40-min) inhibition of viable wheat embryos.

Wheat embryo ribonucleates. X. Metabolism of 3'-hydroxyl termini in the conserved mRNA and tRNA of imbibing wheat embryos

There are conserved complements of ribosomal RNA (rRNA), transfer RNA (tRNA), and messenger RNA (mRNA) in dry wheat embryos. Although early labelling of RNA is largely directed toward the synthesis of complete molecules of nascent rRNA and mRNA, there is also selective labelling at 3′-hydroxyl termini in conserved polynucleotides when dry wheat embryos are subjected to short-term (0.5 h) imbibition in a medium that contains tritium-labelled adenosine, guanosine, cytidine, and uridine. Conserved tRNA is the principal mass component in NaCl-soluble RNA (sRNA) and most of the 'rapid labelling' of sRNA (rl-sRNA) is a result of labelling at 3′-hydroxyl termini in conserved tRNA. By contrast, although conserved rRNA is the principal mass component in NaCl-insoluble RNA (iRNA), most of the labelled 3′-hydroxyl termini in 'rapidly labelled' iRNA (rl-iRNA) do not appear to derive from rRNA. Although about 10% of the labelled 3′-hydroxyl termini in rl-iRNA originates in conserved poly(A)-rich mRNA, the available evidence leads to the conclusion that most of the labelled 3′-hydroxyl termini in rl-iRNA originates in an unusual NaCl-insoluble fraction of conserved tRNA. During the course of extended imbibition, between 0.5 and 5 h, there are characteristic changes in the chain lengths and labelling patterns for 3′-hydroxyl terminal poly(A) sequences in mRNA. Analytical and physiological implications of these data are subjects of discussion.

Wheat embryo ribonucleates. IX. Generation of N2-dimethylguanylate when bulk wheat embryo tRNA is used as substrate for wheat embryo S-adenosylmethionine-tRNA methyltransferases, in vitro

Although the cellular ribonucleates in normally growing cells are virtually saturated with respect to their customary complement of methyl substituents, it has often been reported that 'marginal' levels of (homologous) methylation can be detected when ribonucleates and enzymes from the same source material are incubated, together with S-adenosylmethionine, in vitro. Experiments were designed to acquire new insights that might be useful for circumscribing the number of possible interpretations that could be advanced to account for the introduction of 'supernumerary' methyl groups during (homologous) methylation of wheat RNA by wheat enzymes, in vitro. For a large fraction of the supernumerary methyl groups that can be introduced into wheat RNA, in vitro, it was not possible to adduce convincing evidence in support of the view that any appreciable quantity of methyl groups is ever introduced at these same sites, in vivo. The possibility that these supernumerary methyl groups might have transient existence, in vivo, and the potential physiological significance of any such occurrence are dealt with as part of a more general discussion of the experimental findings.

Wheat embryo ribonucleates. VIII. The presence of 7-methylguanosine 'cap structures' in the RNA of imbibing wheat embryos

1. By imbibing wheat embryos in media that contain methyl-labelled methionine, it is possible to label both terminal and nonterminal 7-methylguanosine constituents in NaCl-insoluble (2.5 M, 0 degrees C) RNA (iRNA). 2. Most of the 7-[Me-14C]methylguanosine in wheat embryo i[Me-14C]RNA is present in nonterminal positions of polynucleotide chains, probably in ribosomal RNA. 3. By passage through a column of oligo-dT-cellulose, it is possible, to show that most of the 7-[Me-3H]methylguanosine in a 'bound' fraction of i[Me-3]RNA from imbibing wheat embryos is present in terminal 'cap' structures, probably in messenger RNA. 4. Although most of the 7-[Me-3H]methylguanosine in the 'unbound' (to oligo-dT-cellulose) fraction of i[Me-3H]RNA was present in nonterminal positions, there was also a highly significant fraction of 7-[Me-3H]methylguanosine in terminal 'cap' structures. Although it will be a subject of continued investigation, possible reasons why a large fraction of the total 7-[Me-3H]-methylguanosine was present in the 'unbound' fraction, in this present study, are a subject of discussion. 5. Careful analysis failed to reveal the presence of any N6,O2'-di[Me-3H]methyladenosine in the 'unbound' fraction of i[Me-3H]RNA. 6. Factors that might influence the binding of 'cap' oligonucleotides to DEAE-cellulose are the subject of a brief discussion.

Wheat embryo ribonucleates. VII. Rapid, efficient and selective formation of 5S-18S and 5.8S-26S hybrids in an aqueous solution of the four ribosomal polynucleotides, and the results of a search for the corresponding hybrids in wheat embryo ribosomes

(1) If wheat embryo 5S and 5.8S rRNA are differentially labelled, it can be shown that there is highly selective association of 5S [14C]RNA with 18S rRNA, and of 5.8S [3H]RNA with 26S rRNA when a solution (0.3 M NaCl) that contains approximately equimolar amounts of the four ribosomal polynucleotides is heated briefly (3 min) at 60 degrees C. (2) Comparison of Tm values and melting profiles for laboratory-prepared and natural 5.8S-26S rRNA hybrids suggests that restoration of the natural union between 5.8S and 26 rRNA can be achieved with facility and fidelity in the laboratory. (3) Union between 5.8S rRNA remains intact when wheat embryo ribosomes are disintegrated either by digestion with pronase or by treatment with sodium dodecyl sulphate, but the same treatments release 5S and 18S rRNA as freely migrating electrophoretic components. (4) Intact 18S and 26S rRNA can be prepared from small and large subunits, respectively, when wheat embryo ribosomes are dissociated by treatment with 0.5 M KCl. (5) Incidental to the principal investigation, it has been shown that, even after storage for more than 6 years at -70 degrees C, commercial supplies of roller-milled wheat germ yield S23 extracts that are very active in the cell-free translation of globin mRNA. (6) The physicochemical and possible biochemical significance of various types of intermolecular complexing between pairs of ribosomal polynucleotides is a subject of discussion.

Wheat embryo ribonucleates. VI. Comparison of the 3'-hydroxyl termini in 'rapidly labelled' RNA from metabolizing wheat embryos with the corresponding termini in ribosomal RNA from differentiating embryos of wheat, barley, corn and pea

The NaCl-insoluble (2.5 M, 0 degrees C) fraction of wheat embryo RNA (iRNA) can be labelled when wheat embryos are subjected to either short-term (0.5 h) or long-term (24 h) imbibition in a medium that contains tritium-labelled adenosine, guanosine, cytidine and uridine. Electrophoretic analyses reveal that, after short-term labelling, there is a broadly heterodisperse distribution of radioactivity in 'rapidly labelled' i[3H]RNA, but after long-term labelling, there is an essentially trimodal distribution of radioactivity in i[3H]RNA. End-group analyses reveal that, after short-term labelling, adenosine is the principal 3'-hydroxyl terminus in all centrifugal subfractions of 'rapidly labelled' i[3H]RNA, whereas cytidine (in 5.8S rRNA), guanosine (in 18S rRNA) and uridine (in 26S rRNA) are the principal 3'-hydroxyl termini in centrifugal subfractions of wheat embryo i[3H]RNA. Guanosine is also the principal 3'-hydroxyl terminus in the 18S rRNA of differentiating embryos excized from both monocotyledonous (wheat, barley, corn) and dicotyledonous (pea) seedlings. The implications that the end-group measurements may have for current views about the possible biochemical involvements of 3'-hydroxyl terminal sequences in both mRNA and 18SrRNA are subjects of discussion. Incidental to the principal investigation, an existing technique for analyzing the RNA contents of cellular materials has been appropriately modified to circumvent interference from uv-absorbing pigments, which, when present, prevent application of the method to plant materials.

The probable 'capping' of wheat leaf messenger ribonucleates by 7-methylguanosine

Experiments have been designed to test the possibility that, as with messenger RNA from animal cells, 7-methylguanosine may be bonded through a pyrophosphate bridge to the 5'-termini of messenger RNA molecules from the cells of a higher-plant organism. It is concluded that 7-methylguanosine is probably bonded through a pyrophosphate bridge to the 5'-termini of messenger RNA molecules from wheat leaves.

Wheat embryo ribonucleates. V. Generation of N2--dimethylguanylate when 'fully sequenced' homogeneous species of transfer RNA are used as substrates for wheat embryo methyltransferases

When S-adenosly[methyl-14-C]methionine and various species of transfer RNA are used as substrates for wheat embryo methyltransferases, the principal site of guanylate-N-2 methylation can be shown to be a G-residue between the stems of the dihydrouridine and anticodon loops. This common site of guanylate-N-2 methylation is referred to as the interstem target site. 2. When the interstem target site is the non-terminal G-residue in a G-C-G-C sequence, as in the cases of Escherichia coli tRNA1-Leu, tRNA-Ile, and tRNA3-Ser, there is preponderant dimethylation to yield N-2-dimethylguanylate. 3. When the interstem target site is part of a U-C-G-U sequence, as in the case of E. coli tRNAf-Met, there is diminished dimethylation and correspondingly increased monomethylation to yield N-2-monomethylguanylate. 4. When the interstem target site is the non-terminal G-residue in an A-U-G-G sequence, as in the case of yeast tRNA-Asp, there is negligible dimethylation and almost exclusive monomethylation to yield N-2-monomethylguanylate. 5. The concerted way in which the primary, secondary, and tertiary structures of tRNA molecules might influence the efficacy of these methylations is the subject of a brief discussion. Attention is also focused on the evolutionary and molecular basis for the generally non-random distributions of methylated oligonucleotide sequences in ribosomal and transfer ribonucleates.

Presence of the methylester of 5-carboxymethyl uridine in the wobble position of the anticodon of tRNAIII Arg from brewer's yeast

The methylester of 5-carboxymethyluridine (mcm5U), its degradation product 5-carboxymethyluridine (cm5U) and the corresponding nucleotide (cm5Up) were isolated from brewer's yeast tRNAIII Arg or from the dodecanucleotide containing the anticodon. Their chromatographic and electrophoretic properties and their UV absorbing spectra were identical to that of the corresponding synthetic compounds. The gas chromatographic behavior and the mass spectrum of mcm5U obtained from tRNAIII Arg and of a synthetic sample were also identical ; the rare occurence of a thermal reciprocal bimolecular methyl-hydrogen transfer in the mass spectrometer ion source was observed. A mild alkaline treatment of tRNAIII Arg leads to the saponification of mcm5U into cm5U (within the tRNA), which can be again esterified in the presence of a yeast homogenate and (methyl-14C) S adenosylmethionine. The radioactivity was found in the mcm5U located in the wobble position of the anticodon of tRNAIII Arg. The presence of this odd nucleotide in that position could possibly restrict the codon-anticodon interaction of tRNAIII Arg.

Wheat-embryo ribonucleates. IV. Factors that influence the formation and stability of a complex between 5S rRNA and 18S rRNA

Under the conditions used in this study, wheat-embryo 5S rRNA complexes with its homologous 18S rRNA from wheat embryos and with heterologous 18S rRNA from other eukaryotic source materials such as yeast, L cells, and HeLa cells, but it does not complex with heterologous 16S rRNA from a prokaryote such as Escherichia coli or with homologous or heterologous 26S (23S) rRNA of either eukaryotic or prokaryotic origin. If a solution of wheat-embryo rRNA is simply made 0.3 M with respect to NaCl and then heated at 60 degress C for 3 min before quick cooling to room temperature (ca. 20 degrees C), there is both preferential and efficient complex formation between 5S and 18S rRNA. The 'laboratory-prepared' complex between wheat-embryo 5S rRNA and its homologous 18S rRNA is more thermostable in 0.1 M NaCl solution than is the 'natural' complexes 'melt' over a narrow range of temperature. The possible physicochemical and physiological importance of both homologous and heterologous rRNA complexes is the subject of a brief discussion.