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R J Cedergren

Publications and source records attributed to R J Cedergren.

At least 19 recordsLinked to original sources
PubMed1988

Total chemical synthesis of a 77-nucleotide-long RNA sequence having methionine-acceptance activity.

Chemical synthesis is described of a 77-nucleotide-long RNA molecule that has the sequence of an Escherichia coli Ado-47-containing tRNA(fMet) species in which the modified nucleosides have been substituted by their unmodified parent nucleosides. The sequence was assembled on a solid-phase, controlled-pore glass support in a stepwise manner with an automated DNA synthesizer. The ribonucleotide building blocks used were fully protected 5'-monomethoxytrityl-2'-silyl-3'-N,N-diisopropylaminophosphoram idites. p-Nitro-phenylethyl groups were used to protect the O6 of guanine residues. The fully deprotected tRNA analogue was characterized by polyacrylamide gel electrophoresis (sizing), terminal nucleotide analysis, sequencing, and total enzyme degradation, all of which indicated that the sequence was correct and contained only 3-5 linkages. The 77-mer was then assayed for amino acid acceptor activity by using E. coli methionyl-tRNA synthetase. The results indicated that the synthetic product, lacking modified bases, is a substrate for the enzyme and has an amino acid acceptance 11% of that of the major native species, tRNA(fMet) containing 7-methylguanosine at position 47.

Base Sequence↗
PubMed1984

On the evolutionary descent of organisms and organelles: a global phylogeny based on a highly conserved structural core in small subunit ribosomal RNA.

To probe the earliest evolutionary events attending the origin of the five known genome types (archaebacterial, eubacterial, nuclear, mitochondrial and plastid), we have analyzed sequences corresponding to a ubiquitous, highly conserved core of secondary structure in small subunit rRNA. Our results support (i) the existence of three primary lineages (archaebacterial, eubacterial, and nuclear), (ii) a specific eubacterial ancestry for plastids and mitochondria (plant, animal, fungal), and (iii) an endosymbiotic, evolutionary origin of the two types of organelle from within distinct groups of eubacteria (blue-green algae (cyanobacteria) in the case of plastids, nonphotosynthetic aerobic bacteria in the case of mitochondria). In addition, our analysis suggests (iv) a biphyletic origin of mitochondria, with animal and fungal mitochondria branching together but separately from plant mitochondria, and (v) a monophyletic origin of plastids. The method described here provides a powerful and generally applicable molecular taxonomic approach towards a global phylogeny encompassing all organisms and organelles.

Animals↗
PubMed1984

The use of cloned tRNA genes for the purification and measurement of specific tRNAs.

We have previously reported the ability of a cloned tRNAMeti gene (pt145) to bind tRNAMeti specifically [5]. In this paper, we show that a pBR322 plasmid containing the tRNAAsn gene of Xenopus (pt38 - donated by Stuart Clarkson) will specifically bind to mouse tRNAAsn when total mouse tRNA, extracted from uninduced Friend erythroleukemia cells, is hybridized to the gene probe. One-dimensional electrophoresis of the hybridizing tRNA in 20% polyacrylamide reveals one major band and several small-molecular-weight minor bands. The hybridizing tRNA has been identified as tRNAAsn by partial RNA sequencing and the detection of both the Q base and t6A. The steady-state concentration of tRNAAsn in the uninduced Friend cell was determined by hybridizing tRNA labeled in vitro to pt38. 1% of the total tRNA hybridized, representing 0.017 pg tRNAAsn/cell. The fraction of newly synthesized tRNA representing tRNAAsn or tRNAMeti was also determined by hybridizing tRNA labeled in vivo to either pt38 or pt145, respectively. 0.96% and 0.85% of the tRNA hybridized to pt38 and pt145, respectively.

Animals↗
PubMed1983

Sequences of halobacterial tRNAs and the paucity of U in the first position of their anticodons.

The sequence of three tRNAs from Halobacterium cutirubrum have been determined. The sequences of tRNAValGAC and tRNAValCAC differ by only one nucleotide which is in the 5' terminal anticodon position. These tRNAs as well as that of tRNAAlaCGC are compared to other known halobacterial tRNAs. An observed paucity (or absence) of U in the first anticodon position is unique to archaebacterial tRNAs and may be indicative of unusual decoding properties of these organisms.

Anticodon↗
PubMed1983

The isolation and measurement of tRNAmeti using RNA/DNA hybridization.

A pBR322 plasmid containing the initiator tRNAmet gene of Xenopus (pt145 - donated by Stuart Clarkson) will specifically bind to mouse initiator tRNAmet (tRNAmeti) when total mouse tRNA, extracted from uninduced Friend erythroleukemia cells, is hybridized to the gene probe. One dimensional electrophoresis of the hybridizing tRNA in 20% polyacrylamide reveals one major band (95%) and a minor band. The hybridizing tRNA has been identified as initiator tRNAmet by RNA sequencing. Hybridization of tRNAtotal to another plasmid containing the Xenopus gene for tRNAasn results in two bound species with different electrophoretic mobilities than the tRNA bound to the initiator tRNAmet gene. pt145 has been used to measure the steady state concentration of initiator tRNAmet in the uninduced and erythroid Friend cell, and in the unfertilized egg and 21 h blastula of the sea urchin. Initiator tRNAmet represents 0.91% and 0.52% of the tRNA populations extracted from uninduced and erythroid Friend cells, respectively. Based upon the total tRNA content per cell, there is a 3.8 fold decrease in initiator tRNAmet per cell during erythroid differentiation. tRNA extracted from unfertilized eggs and 21 h blastula of the sea urchin both have 0.5% of total tRNA as initiator tRNAmet (approximately 1.5 pg).

Animals↗
PubMed1982

An algorithm for the display of nucleic acid secondary structure.

A simple algorithm is presented for the graphic display of nucleic acid secondary structure. Examples of secondary structure displays are given for tRNA, 5S RNA and part of the 16S RNA. Due to its speed, this algorithm could easily be used in conjunction with secondary structure programs which calculate various alternate structures.

Base Sequence↗
PubMed1982

5S RNA sequence from the Philosamia silkworm: evidence for variable evolutionary rates in insect 5S RNA.

The primary structure of 5S RNA isolated from the posterior silkgland of Philosamia cynthia ricini was determined using three in vitro labelling techniques. The derived sequence consists of 119 nucleotides and can be folded into the secondary structure model proposed for eukaryotic 5S RNAs. This 5S RNA differs from the Bombyx mori molecule in 9 positions and from the Drosophila melanogaster sequence in 14 positions. The comparison of evolutionary rates in insect 5S RNA with inferred rates in other eukaryotic phyla leads to the conclusion that 5S RNA evolution is not constant in different eukaryotic branches, a condition which must be taken into account in phylogenetic tree constructions.

Animals↗
PubMed1982

A strategy for sequence phylogeny research.

Minimal mutation trees, and almost minimal trees, are constructed from two data sets, one of phenylalanine tRNA sequences, and the other of 5S RNA sequences, from a diverse range of organisms. The two sets of results are mutually consistent. Trees representing previous evolutionary hypotheses are compared using a total weighted mutational distance criterion. The importance of sequence data from relatively little-studed phylogenetic lines is stressed. A procedure is illustrated which circumvents the computational difficulty of evaluating the astronomically large number of possible trees, without resorting to suboptimal methods.

Bacteria↗
PubMed1982

Structure in tRNA data.

260 sequences of tRNA are compared, after their classification into six categories: prokaryotic (83 sequences) and eukaryotic (83 sequences) elongators, prokaryotic (10 sequences) and eukaryotic (11 sequences), initiators, lower eukaryotic mitochondrial tRNA (53 sequences) and archaebacterial tRNA (20 sequences). Beside the presence of invariable and semi-invariable positions in tRNA, non-random base distribution in almost all positions is also evident; most of them being characteristic of each class of tRNA. Therefore, during evolution it would seem that selectional pressures do act in so called variable positions as well as invariant positions of tRNA molecules. Results are discussed in relation to possible restrictions depending on functional and/or structural constraints of tRNA.

Animals↗
PubMed1982

An evaluation of mitochondrial tRNA gene evolution and its relation to the genetic code.

Extensive sequence data on mitochondrial (mt) tRNAs give for the first time an opportunity to evaluate tRNA gene evolution in this organelle. Deductions from these gene structures relate to the evolution of tRNA genes in other cellular systems and to the origin of the genetic code. Mt tRNAs, in contrast to the prokaryotic nature of chloroplastic tRNA structure, can not at the present time be definitely related to either prokaryotic or eukaryotic tRNAs, probably because of a higher mutation rate in mitochondria. Fungal mt tRNAs having the same anticodon and function are generally similar enough to be considered homologous. Comparisons af all mt tRNA sequences contained in the same mitochondrion indicate that some tRNAs originated by duplication of a prototypic gene which, after divergence, led to tRNAs having different amino acid specificities. The deviant mt genetic code, although admittedly permitting a simpler decoding mechanism, is not useful in determining whether the origin of mitochondria had preceded or was derived from prokaryotes or eukaryotes, since the genetic code is variable even among mitochondria. Variants of the mt genetic code lead to speculation on the nature of the primordial code and its relation to the present "universal" code.

Animals↗
PubMed1981

The evolution of multi-isoacceptor tRNA families. Sequence of tRNA Leu CAA and tRNA Leu CAG from Anacystis nidulans.

Two leucine tRNAs from the cyanophyte Anacystis nidulans have been isolated, and their complete nucleotide sequences have been determined by combining data from oligonucleotide fingerprints and sequencing gels. The two sequences are 87 nucleotides long, have the anticodons CAA and CAG, and differ from each other at a total of 28 positions. They have been compared to other known tRNA Leu sequences and incorporated into a phylogenetic tree comprising prokaryotic and chloroplastic tRNA Leu sequences. Mutations inferred from the tree show that some parts of the tRNA molecule are highly variable (the extra arm and the acceptor stem) while others are much more conserved (the D and T arms). The topology of the tree supports the idea that blue-green algae and chloroplasts share a common prokaryotic ancestor and show a basic divergence between XAA and XAG anticodon-containing tRNAs, suggesting that these two subfamilies result from an ancient gene duplication. Finally, comparison of this phylogenetic tree with those of other multi-isoacceptor tRNA families shows no common scheme, which may be due to independent refinement of codon-reading patterns in different tRNA families.

Base Sequence↗
PubMed1981

The evolving tRNA molecule.

The study of tRNA molecular evolution is crucial to understanding the origin and establishment of the genetic code as well as the differentiation and refinement of the machinery of protein synthesis in prokaryotes, eukaryotes, organelles, and phage systems. The small size of the molecule and its critical involvement in a multiplicity of roles distinguish its study from classical protein molecular evolution with respect to goals and methods. Here, the authors assess available and missing data, existing and needed methodology, and the impact of tRNA studies on current theories both of genetic code evolution and of the evolution of species. They analyze mutational "hot spots", the role of base modification, synthetase recognition, codon-anticodon interactions and the status of organelle tRNA.

Animals↗
PubMed1980

Convergence and minimal mutation criteria for evaluating early events in tRNA evolution.

The convergence of ancestral sequences independently constructed from different branches of a phylogenetic tree can be used as a test of homology of data sequences. This criterion has shown that all phenylalanine tRNAs are related to a common ancestor, whereas eukaryotic and prokaryotic tyrosine tRNAs may have independent origins. All glycine tRNAs share a common ancestor. The glycine tRNA family splits according to the purine or pyrimidine nature of the first anticodon base prior to the divergence of eukaryotes and prokaryotes. The structural similarity between some prokaryotic glycine and and valine tRNAs is the result of their derivation from a common ancestor that existed previous to the divergence of the different glycine tRNAs. These results support models of genetic code evolution involving the incremental elaboration of earlier, simpler codes.

Animals↗
PubMed1979

Evolution of methionine initiator and phenylalanine transfer RNAs.

Sequence data from methionine initiator and phenylalanine transfer RNAs were used to construct phylogenetic trees by the maximum parsimony method. Although eukaryotes, prokaryotes and chloroplasts appear related to a common ancestor, no firm conclusion can be drawn at this time about mitochondrial-coded transfer RNAs. tRNA evolution is not appropriately described by random hit models, since the various regions of the molecule differ sharply in their mutational fixation rates. "Hot" mutational spots are identified in the Tpsic, the amino acceptor and the upper anticodon stems; the D arm and the loop areas on the other hand are highly conserved. Crucial tertiary interactions are thus essentially preserved while most of the double helical domain undergoes base pair interchange. Transitions are about half as costly as transversions, suggesting that base pair interchanges proceed mostly through G-U and A-C intermediates. There is a preponderance of replacements starting from G and C but this bias appears to follow the high G + C content of the easily mutated base paired regions.

Animals↗
PubMed1979

Distinctive properties of glutamine synthetase from the cyanobacterium Anacystis nidulans.

The intracellular levels of glutamine synthetase (GS) in Anacystis nidulans grown under different conditions were determined using a whole-cell assay. Nitrate-grown cells have 64% more GS than cells grown in ammonium sulfate. Nitrogen starvation does not affect GS levels appreciably. Incubation of nitrate-grown cells with ammonium sulfate does not change the ratio of gamma-glutamyl transferase activities stimulated by Mg2+ and Mn2+ ions. An in vitro test of adenylylation indicates that algae do not have an endogenous adenylyl transferase (ATase) and that algal GS is not adenylylatable by the Klebsiella aerogenes ATase. Some characteristics of the GS-membrane complex were determined by centrifugation of the complex under varying conditions of pH and ionic strength. In this way, it was shown that acid pH (4.5) stabilizes the complex and high ionic strength tends to solubilize the enzyme. A simple partial purification of GS (89-fold) was developed based on the sedimentation properties of GS.

Cell Membrane↗
PubMed1978

Bacteriophage MS2 RNA: a correlation between the stability of the codon: anticodon interaction and the choice of code words.

The non-random distribution of degenerate code words in Bacteriophage MS2 RNA can be explained partially by considerations of the stability of the codon-anticodon complex in prokaryotic systems. Supporting this hypothesis we note that wobble codons are positively selected in codons having G and/or C in the first two positions. In contrast, wobble codons are statistically less likely in codons composed of A and U in the first two positions. Analyses of nucleotides adjacent to 5' and 3' ends of codons indicate a nonrandom distribution as well. It is thus likely that some elements of RNA evolution are independent of the structural needs of the RNA itself and of the translated protein product.

Anticodon↗
PubMed1978

Alterations in lysine transfer RNA during erythroid differentiation of the Friend cell.

The proportion of lysine tRNA represented by the isoacceptor species lysine tRNA4 has previously been shown to be largest in cells with the greatest ability to proliferate. Using reverse phase chromatography (RPC-5), we have analyzed the changes in the relative quantities of lysine tRNA species which occur in different cellular states of the Friend cell, a transformed murine cell infected with Friend erythroleukemia virus complex. This cell undergoes erythroid differentiation when exposed to various chemicals. Lysine tRNA4 comprises 32% of the total lysine tRNA in rapidly dividing, uninduced Friend cells, but only 16% of the total lysine tRNA in uninducase. Friend cells undergoing erythroid differentiation divide more slowly than uninduced cells, and finally cease proliferation, but lysine tRNA4 becomes the major lysine tRNA species (greater than 50%). This does not appear to reflect erythroid properties of the cell, since the lysine tRNA of the mouse reticulocyte contains very little lysine tRNA4. The non-dividing erythroid Friend cell, therefore, represents an exception to the finding that non-dividing cells usually have little or no lysine tRNA4 present.

Animals↗