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R Cedergren

Publications and source records attributed to R Cedergren.

At least 37 records · Page 2Linked to original sources
PubMed1989

Evolution of a tRNA operon in gamma purple bacteria.

Genomic DNA from eubacteria belonging to the gamma-3 subdivision of purple bacteria, as classified by Woese (C.R. Woese, Microbiol. Rev. 51:221-271, 1987), were probed with the argT operon of Escherichia coli encoding 5'-tRNA(Arg)-tRNA(His)-tRNA(Leu)-tRNA(Pro)-3'. The homologous operon from Vibrio harveyi was isolated and sequenced. Comparison of the five available sequences of this tRNA cluster from members of the families Enterobacteriaceae, Aeromonadaceae, and Vibrionaceae led to the conclusion that variations in different versions of this operon arose not only by point mutations but also by duplication and addition-deletion of entire tRNA genes. This data base permitted the formulation of a proposal dealing with the evolutionary history of this operon and suggested that DNA regions containing tRNA genes are active centers (hot spots) of recombination. Finally, since the operon from V. harveyi was not highly repetitive and did not contain tRNA pseudogenes, as in the Photobacterium phosphoreum operon, hybridization of genomic DNAs from different photobacterial strains with probes specific for the repeated pseudogene element was performed. We conclude that the phylogenetic distribution of the repetitive DNA is restricted to strains of P. phosphoreum.

Base Sequence↗
PubMed1988

The relationship between RNA catalytic processes.

Proposals that an RNA-based genetic system preceded DNA, stem from the ability of RNA to store genetic information and to promote simple catalysis. However, to be a valid basis for the RNA world, RNA catalysis must demonstrate or be related to intrinsic chemical properties which could have existed in primordial times. We analyze this question by first classifying RNA catalysis and related processes according to their mechanism. We define: (A) the disjunct nucleophile class which leads to 5'-phosphates. These include Group I and II intron splicing, nuclear mRNA splicing and RNase P reactions. Although Group I introns and its excision mechanism is likely to have existed in primordial times, present-day examples have arisen independently in different phyla much more recently. Comparative methodology indicates that RNase P catalysis originated before the divergence of the major kingdoms. In addition, all disjunct nucleophile reactions can be interrelated by a proposed mechanism involving a distant 2-OH nucleophile. (B) the conjunct nucleophile class leading to 3'-phosphates. This class is composed of self-cleaving RNAs found in plant viruses and the newt. We propose that tRNA splicing is related to this mechanism rather than the previous one. The presence of introns in tRNA genes of eukaryotes and archaebacteria supports the idea that tRNA splicing predates the divergence of these cell types.

Animals↗
PubMed1988

Tandemly repeated tRNA pseudogenes in photobacterium.

A region distal to three tRNA genes in Photobacterium phosphoreum, a Gram-negative eubacterium, unexpectedly contains a high number of repeated DNA segments that are closely related to the adjacent tRNAPro gene. The 5' to 3' order of this cluster is tRNAPro-tRNAHis-tRNAPro followed by eight tRNAPro-like structures interspersed by rho-independent terminators. The two tRNAPro genes, which are identical, and the tRNAHis gene have 86% and 87% positional identity, respectively, to their counterparts in the argT operon of Escherichia coli. The facts that these tRNA-like structures are not transcribed, in contrast to the tRNA retropseudogenes of eukaryotes, and that these structures are clustered near their progenitor suggest they are an unusual class of tRNA pseudogenes that arose by tandem duplication.

Base Sequence↗
PubMed1988

A secondary and tertiary structure editor for nucleic acids.

A major difficulty in the evaluation of secondary and tertiary structures of nucleic acids is the lack of convenient methods for their construction and representation. As a first step in a study of the symbolic representation of biopolymers, we report the development of a structure editor written in Pascal, permitting model construction on the screen of a personal computer. The program calculates energies for helical regions, allows user-defined helices and displays the secondary structure of a nucleic acid based on a user-selected set of helices. Screen and printer outputs can be in the form of a backbone or the letters of the primary sequence. The molecule can then be displayed in a format which simulates its three-dimensional structure. Using appropriate glasses, the molecule can be viewed on the screen in three dimensions. Other options include the manipulation of helices and single-stranded regions which results in changes in the spatial relationship between different regions of the molecule. The editor requires an IBM or compatible PC, 640 kbyte memory and a medium or high resolution graphics card.

Algorithms↗
PubMed1988

FUS: a system to simulate conformational changes in biological macromolecules.

In order to study the dynamics of protein and nucleic acid conformations, a molecular folding-unfolding system (FUS written in Lisp) has been developed. Secondary structure features of protein and nucleic acids are graphically represented by cubes in a modified 'Blocks World' paradigm. Modeling of protein and nucleic acid unfolding (denaturation) and folding of their three-dimensional structure is possible by the use of high level 'block' operators which allow displacement of these structural features in space. Due to the flexible nature of this program, FUS is a useful tool for the rapid evaluation of user-defined rules governing conformational changes. The use of FUS to unfold three common proteins (prealbumin, flavodoxin and triose phosphate isomerase) and a tRNA is presented.

Computer Simulation↗
PubMed1988

Highly repetitive tRNA(Pro)-tRNA(His) gene cluster from Photobacterium phosphoreum.

A DNA fragment comprising the four tRNA gene sequences of the Escherichia coli argT locus hybridized with two Sau3A-generated DNA fragments from the vibrio Photobacterium phosphoreum (ATCC 11040). Detailed sequence analysis of the longer fragment shows the following gene organization: 5'-promoter-tRNA(Pro)-tRNAPro-tRNA(Pro)-tRNA(His)-tRNA(Pro)-tRNA(Pro)- tRNA(His)-tRNA(Pro)-five pseudogenes derived from the upstream tRNAPro interspersed by putative Rho-independent terminators. This sequence demonstrates the presence of highly repetitive, tandem tRNA genes in a bacterial genome. Furthermore, a stretch of 304 nucleotides from this cluster was found virtually unchanged in the other (shorter) fragment which was previously sequenced. The two clusters together contain eight tRNA(Pro) pseudogenes and eight fully intact tRNA(Pro) genes, an unusually high number for a single eubacterial isoacceptor tRNA. These results show that the organization of some tRNA operons is highly variable in eubacteria.

Base Sequence↗
PubMed1987

A mechanism for the RNA-catalyzed formation of 5'-phosphates. The origin of nucleases.

Processes involved in RNA metabolism can be distinguished by the nature of the sugar phosphate substitution (5' or 3') in intermediates or products. Although it is known that 3'-phosphates are produced via a 2',3'-cyclic phosphate intermediate, formed by nucleophilic attack on the phosphodiester bond by the adjacent 2'-OH, little is known about the production of 5'-phosphate products. We attribute 5'-phosphate intermediates and products to a preferred configuration of the pentavalent phosphorus intermediate resulting from the attack of a distant nucleophile. This intermediate is favored, since its formation is possible without major conformational changes in the molecule. Based on the two products of nucleic acid hydrolysis we define: the conjunct and disjunct nucleophile mechanisms, each of which would have independent origins. Indeed, the products of an overwhelming number of nucleases and RNases are consistent with one of these mechanistic models demonstrating that the origin of these enzymes are deeply rooted in the intrinsic chemistry of phosphate esters.

Catalysis↗
PubMed1987

The mitochondrial genome of the fission yeast, Schizosaccharomyces pombe. Sequence of the large-subunit ribosomal RNA gene, comparison of potential secondary structure in fungal mitochondrial large-subunit rRNAs and evolutionary considerations.

The DNA sequence of the mitochondrial large subunit (LSU) rRNA gene of Schizosaccharomyces pombe has been determined. In the direction of transcription, this gene is located between the gene coding for subunit II of cytochrome oxidase and a cluster of three tRNA genes. Both the 5' and 3' ends of the LSU rRNA have been mapped precisely: whereas the 5' end can be assigned unambiguously to a single nucleotide position, multiple 3' ends occur within a run of eight U residues. Based on these results, the S. pombe LSU rRNA is between 2818 and 2826 nucleotides long. A sequence motif immediately upstream of the 5' end of the gene resembles that of the mitochondrial promoter motif of Saccharomyces cerevisiae; however, the sequence at the 3' end of the gene is not similar to any of the motifs implicated as processing signals in other mitochondrial systems. Unlike its counterparts in S. cerevisiae and Aspergillus nidulans, the mitochondrial LSU rRNA gene of S. pombe does not contain an intron. Comparison of potential secondary structure among the three fungal mitochondrial and Escherichia coli LSU rRNAs has defined a common secondary structure core, held together by long-range hydrogen-bonding interactions. A 5.8S-like structure is present within the 5'-terminal region of all three fungal mitochondrial LSU rRNAs; in contrast, no 4.5S-like structure is evident at the 3' end of these molecules. An evolutionary evaluation of highly conserved regions of a small set of LSU rRNA sequences suggests that S. pombe mitochondria diverged from a mitochondrial proto-fungal branch earlier than either A. nidulans or S. cerevisiae mitochondria. This result, considered in conjunction with the patterns of genome organization and codon usage in fungal mitochondria, points to a slower evolutionary clock speed in the mitochondrial genome of S. pombe.

Base Sequence↗
PubMed1987

The in vivo stability, maturation and aminoacylation of anticodon-substituted Escherichia coli initiator methionine tRNAs.

We have constructed eight anticodon-modified Escherichia coli initiator methionine (fMet) tRNAs by insertion of synthetic ribotrinucleotides between two fragments ('half molecules') derived from the initiator tRNA. The trinucleotides, namely CAU (the normal anticodon), CAA, CAC, CAG, GAA, GAC, GAG and GAU, were joined to the 5' and 3' tRNA fragments with T4 RNA ligase. The strategy of reconstruction permitted the insertion of radioactive 32P label between nucleotides 36 and 37. tRNAs were microinjected into the cytoplasm of Xenopus laevis oocytes, and the following properties were evaluated: the stability of these eubacterial tRNA variants in the eukaryotic oocytes; the enzymatic modification of the adenosine at position 37 (3' adjacent to the anticodon) and aminoacylation of the chimeric tRNAs by endogenous oocyte aminoacyl-tRNA synthetases. In contrast to other variants, the two RNAs having CAU and GAU anticodons were stable and underwent quantitative modification at A-37. These results show that the enzyme responsible for the modification of A-37 to N-[N-(9-beta-D-ribofuranosylpurine-6-yl)carbamoyl]threonine (t6A) is present in the cytoplasm of oocytes and is very sensitive to the anticodon environment of the tRNA. Also, these same GAU and CAU anticodon-containing tRNAs are fully aminoacylated with the heterologous oocyte aminoacyl-tRNA synthetases in vivo. During the course of this work we developed a generally applicable assay for the aminoacylation of femtomole amounts of labelled tRNAs.

Animals↗
PubMed1987

Archetypical features in tRNA families.

A compilation of known tRNA, and tRNA gene sequences from archaebacteria, eubacteria, and eukaryotes permits the construction of tRNA cloverleafs which show conserved structural elements for each tRNA family. Positions conserved across the three kingdoms are thought to represent archetypical features of tRNAs which preceded the divergence of these kingdoms.

Archaea↗
PubMed1987

On the primacy of primordial RNA.

The ability of RNA to catalyze biochemical reactions is used to develop a self-consistent picture of how a primordial RNA could have given rise to the necessary factors and processes of early life forms. Essential to this proposal is the impact of RNA structural domains, "selected" by thermodynamic criteria, on the structure of early proteins (exons) and the assembly of functional complexes. Based on this analysis, the chronological appearance of informational molecules follows the order: primordial RNA, proteins whose structures are determined by primordial RNA sequences and finally DNA.

Biological Evolution↗
PubMed1987

Site-directed protection of RNA during nuclease digestion.

We report the use of oligodeoxynucleotides to block the nucleolytic hydrolysis of single-stranded regions of RNA. Using complementary oligomers, the hydrolysis of the CCA terminus of methionine initiator tRNA could be prevented. This method can be useful in the production of specific single-stranded fragments of RNA, which are necessary in recombinant RNA technology.

Base Sequence↗
PubMed1987

Restriction of single-stranded M13 DNA using synthetic oligonucleotides: the structural requirement of restriction enzymes.

A targeted ss (single stranded) DNA cleavage technique is reported which involves the use of synthetic oligomers complementary to the ss M13 DNA polylinker. BamHI, SmaI, and KpnI restriction enzymes were tested with a partial duplex DNA formed from ss M13 DNA and a nested series of fragments derived from a synthetic 21-mer which were complementary to the polylinker region. These enzymes require up to two flanking nucleotides in addition to the hexameric recognition site for efficient cleavage. This technique could be useful for effecting unique cleavages of DNA with enzymes which generally give a large number of fragments and for strategies of ss DNA manipulation.

Base Sequence↗
PubMed1987

RNA design by in vitro RNA recombination and synthesis.

The techniques of in vitro RNA synthesis and recombination are presented. These include the site-specific cleavage of RNA, the manipulation of terminal phosphates, and the ligation of RNA fragments. Areas of promising future research include the establishment of RNA cloning vectors and the use of in vitro transcription of natural or designed RNA genes. The chemical synthesis approach now offers the possibility of making large amounts of biologically active length RNAs and of incorporating modified or reporter nucleotides into RNA sequences for physical studies. The new RNA techniques taken with DNA technology will permit a new approach towards understanding the complexity of RNA metabolism and the relationship of structure to function in RNAs.

Base Sequence↗
PubMed1986

Natural selection versus primitive gene structure as determinant of codon usage.

Different codons are not utilized equally in known gene sequences. One of the important biases of codon usage is observed in the form of an enrichment of RNY codons, especially within RNN codon families. Such biases could represent the residue of a primitive repeating-RNY gene structure, or the outcome of natural selection, or both. Analyses based on the rates of silent substitutions, the frequencies of base doublets, and synonymous codon ratios for Escherichia coli, yeast, Drosophila and Xenopus proteins have been performed. The results rule out any significant support for a primitive repeating-RNY or repeating-RRY gene structure, and establish the important role of natural selection in determining the choice of codons. With strong intervention by natural selection, the relationship between primitive gene structure and codon usage necessarily becomes minimal.

Animals↗
PubMed1986

Primordial reading of genetic information.

From the consideration of general features of the anticodon loop and stem in tRNA and the properties of present-day translation, we put forward a plausible scenario to explain the evolution of the genetic code from a highly ambiguous triplet code to the present refined decoding system. Our model based on the reading of the code suggests that the anticodon of primordial tRNA could adopt either the 3' or the 5' stacked conformation permitting the formation of the "best two out of three" base pairs, either the first and second codon position or the second and third. Progressive acquisition of precise structural constraint and the modification of bases in the anticodon loop would give way eventually to the less ambiguous "two out of three" reading mechanism having only the 3' stacked conformation. Further adjustments of base composition and modification leads inevitably to the present generalized code. In this way the primordial code encoding 4-8 amino acids or related derivates evolves smoothly to the present code having 20 amino acids.

Biological Evolution↗
PubMed1985

Nucleotide sequences of two serine tRNAs with a GGA anticodon: the structure-function relationships in the serine family of E. coli tRNAs.

We have determined the nucleotide sequence of the major species of E. coli tRNASer and of a minor species having the same GGA anticodon. These two tRNAs should recognize the UCC and UCU codons, the most widely used codons for serine in the highly expressed genes of E. coli. The two sequences differ in only one position of the D-loop. Neither tRNA has a modified adenosine in the position 3'-adjacent to the anticodon. This can be rationalized on the basis of a structural constraint in the anticodon stem and may be related to optimization of the codon-anticodon interaction. Comparison of all E.coli serine tRNAs (and that encoded by bacteriophage T4) reveals characteristic (possibly functional) features. Evolutionary analysis suggests an eubacterial origin of the T4 tRNASer gene and the existence of a recent common ancestor for the tRNASerGGA and tRNASerGUC genes.

Anticodon↗