Nucleotide Sequence of Pseudomonas fluorescens 5 S Ribonucleic Acid

The discovery of archaea: from observed anomaly to consequential restructuring of the phylogenetic tree

Observational and experimental discoveries of new factual entities such as objects, systems, or processes, are major contributors to some advances in the life sciences. Yet, whereas discovery of theories was extensively deliberated by philosophers of science, very little philosophical attention was paid to the discovery of factual entities. This paper examines historical and philosophical aspects of the experimental discovery by Carl Woese of archaea, prokaryotes that comprise one of the three principal domains of the phylogenetic tree. Borrowing Kuhn's terminology, this discovery of a major biological entity was made during a 'normal science' project of building molecular taxonomy for prokaryotes. Unexpectedly, however, an observed anomaly instigated the discovery of archaea. Substantiation of the existence of the new archaeal entity and consequent reconstruction of the phylogenetic tree prompted replacement of a long-held model of a prokarya and eukarya bipartite tree of life by a new model of a tripartite tree comprising of bacteria, archaea, and eukarya. This paper explores the history and philosophical implications of the progression of Woese's project from normal science to anomaly-instigated model-changing discovery. It is also shown that the consequential discoveries of RNA splicing and of ribozymes were similarly prompted by unexpected irregularities during normal science activities. It is thus submitted that some discoveries of factual biological entities are triggered by unforeseen observational or experimental anomalies.

Molecular phylogenetics before sequences: oligonucleotide catalogs as k-mer spectra

From 1971 to 1985, Carl Woese and colleagues generated oligonucleotide catalogs of 16S/18S rRNAs from more than 400 organisms. Using these incomplete and imperfect data, Carl and his colleagues developed unprecedented insights into the structure, function, and evolution of the large RNA components of the translational apparatus. They recognized a third domain of life, revealed the phylogenetic backbone of bacteria (and its limitations), delineated taxa, and explored the tempo and mode of microbial evolution. For these discoveries to have stood the test of time, oligonucleotide catalogs must carry significant phylogenetic signal; they thus bear re-examination in view of the current interest in alignment-free phylogenetics based on k-mers. Here we consider the aims, successes, and limitations of this early phase of molecular phylogenetics. We computationally generate oligonucleotide sets (e-catalogs) from 16S/18S rRNA sequences, calculate pairwise distances between them based on D₂ statistics, compute distance trees, and compare their performance against alignment-based and k-mer trees. Although the catalogs themselves were superseded by full-length sequences, this stage in the development of computational molecular biology remains instructive for us today.

500-MHz proton homonuclear Overhauser evidence for additional base pair in the common arm of eukaryotic ribosomal 5S RNA: wheat germ

A "common-arm" fragment from wheat germ (Triticum aestivum) 5S RNA has been produced by enzymatic cleavage with RNase T1 and sequenced via autoradiography of electrophoresis gels for the end-labeled fragments obtained by further RNase T1 partial digestion. The existence, base pair composition, and base pair sequence of the common arm are demonstrated for the first time by means of proton 500-MHz nuclear magnetic resonance. From Mg2+ titration, temperature variation, ring current calculations, sequence comparisons, and proton homonuclear Overhauser enhancement experiments, additional base pairs in the common arm of the eukaryotic 5S RNA secondary structure are detected. Two base pairs, G41 X C34 and A42 X U33 in the hairpin loop, could account for the lack of binding between the conserved GAAC segment of 5S RNA and the conserved Watson-Crick-complementary GT psi C segment of tRNAs.

Open and closed 5 S ribosomal RNA, the only two universal structures encoded in the nucleotide sequences

The nucleotide sequences of small ribosomal RNA (5 S rRNA) molecules of different organisms are presumably designed to ensure folding of these molecules in some standard secondary structure(s). To extract this message contained in the sequences we have plotted the triangular matrix diagrams of all potential hairpins for 44 representative 5 S rRNA sequences. Subjecting these diagrams to simple image-processing procedures we have found that only five hairpins are universally present in all known 5 S rRNA molecules. Two of these hairpins share the same stretch of the nucleotide sequence, others being independent. Thus, only two major secondary structures of 5 S rRNA can be formed. These are of the well-known Y-like (open) form and a novel P-like form closed by the tertiary interaction which involves two complementary stretches four to seven bases long.

Conservation of secondary structure in 5 S ribosomal RNA: a uniform model for eukaryotic, eubacterial, archaebacterial and organelle sequences is energetically favourable

The most commonly accepted secondary structure models for 5S RNA differ for molecules of eubacterial origin, where the four-helix model of Fox and Woese is generally cited, and those of eukaryotic origin, where a fifth helix is assumed to exist. We have carefully aligned all available sequences from eukaryotes, eubacteria, chloroplasts, archaebacteria and plant mitochondria. We could thus derive a unified secondary structure model applicable to all 5S RNA sequences known to-date. It contains the five helices already present in the eukaryotic model, extended by additional segments that were not previously assumed to be universally present. One of the helices can be written in two equilibrium forms, which could reflect the existence of a flexible, dynamic structure. For the derivation of the model and the estimation of the free energies we followed a set of rules optimized to predict the tRNA cloverleaf. The stability of the unified model is higher than that of nearly all previously proposed sequence-specific and general models.

Partial enzyme digestion studies on Escherichia coli, Pseudomonas, Chlorella, Drosophila, HeLa and yeast 5S RNAs support a general class of 5S RNA models

Fox and Woese (1975a) have shown that a model of 5S RNA secondary structure similar to the one originally derived for Chlorella 5S RNA can be generalized with relatively minor variations to all sequenced 5S RNA molecules, i.e. that corresponding base paired regions can be formed at approximately the same positions. We present experimental data in favour of this hypothesis and show that the points at which ribonucleases T1, T2 and pancreatic ribonuclease cleave six different 5S RNA molecules under 'mild' conditions (high ionic strength, low temperature, low RNAase concentration) nearly always fall in the proposed single-stranded regions. We conclude that this model is a good approximation to the conformation of 5S RNA in solution.

Human globin messenger RNA: importance of cloning for structural analysis

The sequence of most of the human beta globin messenger RNA and large sections of the alpha globin messenger RNA has been determined. Partly because of genetic polymorphism, it was necessary to clone globin complementary DNA in order to extend the analysis. Purified human fetal globin messenger RNA was isolated and used as a template by reverse transcriptase to produce duplex complementary DNA molecules. These molecules were linked in vitro to plasmid DNA by use of T4 ligase in the presence of Escherichia coli Pol 1. Several colonies transformed by these molecules have been shown to hybridize with labeled human globin complementary RNA.

Occurrence in Bacillus licheniformis of two species of 5-S RNA with multiple differences in primary structure

Bacillus licheniformis was found to contain two species of 5-S RNA. One of these, the primary structure of which has been published previously [H. A. Raué, T.J. Stoof and R.J. Planta (1975) Eur. J. Biochem. 59, 35--42] accounts for 80--90% of the total cellular amount of 5-S RNA. The other one, comprising 10--20% of the total amount, differs in primary structure from the major species at eight positions. All base changes are either purine leads to purine or pyrimidine leads to pyrimidine substitutions. Half of the changes are located within the 5'-terminal part (15 nucleotides) of the molecule, the other half in the 3'-terminal region (22 nucleotides). At least one of the base changes is in a region which in B. subtilis has been implicated in processing of precursor 5-S RNA. The data are consistent with the existence of a single 5-S RNA cistron with a primary structure different from that of all other 5-S RNA cistrons in B. licheniformis.

Sequence characterization of 5S ribosomal RNA from eight gram positive procaryotes

The available comparative data on procaryotic 5S rRNA was extended through sequencing studies of eight gram positive procaryotes. Complete nucleotide sequences were presented for 5S rRNA from Bacillus subtilis, B. firmus, B. pasteurii, B. brevis, Lactobacillus brevis and Streptococcus faecalis. In addition, 5S rRNA oligonucleotide catalogs and partial sequence data were provided for B. cereus and Sporosarcina ureae. These sequences and catalogs were discussed in terms of known features of procaryotic 5S rRNA architecture.

Frequency of insertion-deletion, transversion, and transition in the evolution of 5S ribosomal RNA

The problem of choosing an alignment of two or more nucleotide sequences is particularly difficult for nucleic acids, such as 5S ribosomal RNA, which do not code for protein and for which secondary structure is unknown. Given a set of 'costs' for the various types of replacement mutations and for base insertion or deletion, we present a dynamic programming algorithm which finds the optimal (least costly) alignment for a set of N sequences simultaneously, where each sequence is associated with one of the N tips of a given evolutionary tree. Concurrently, protosequences are constructed corresponding to the ancestral nodes of the tree. A version of this algorithm, modified to be computationally feasible, is implemented to align the sequences of 5S RNA from nine organisms. Complete sets of alignments and protosequence reconstructions are done for a large number of different configurations of mutation costs. Examination of the family of curbes of total replacements inferred versus the ratio of transitions/transversions inferred, each curve corresponding to a given number of insertions-deletions inferred, provides a method for estimating relative costs and relative frequencies for these different types of mutations.

Thermal denaturation of mesophilic and thermophilic 5S ribonucleic acids

The Tm of Bacillus stearothermophilus 5S ribonucleic acid (RNA) is 1.5 +/- 0.5 C higher than that of 5S RNAs from B. subtilis and Escherichia coli. Melting in 50% methanol and in formaldehyde indicate that both base stacking and helical regions are involved in the slightly increased thermal stability of B. stearothermophilus 5S RNA. It is probable that the 5S RNA makes only a minor contribution to the thermostability of B. stearothermophilus 50S ribosomal subunits.

Evolution of 5sRNA

The evolution of 5sRNA of 17 organisms ranging from human to bacteria has been studied using a sequence homology analysis. The evolutionary rate of 5sRNA genes has been estimated to be 2.2x10(-10) replacement per one nucleotide site per year. This value is about the same as that of cytochrome C or tRNA's (congruent to 2x10(-10)). A phylogenic tree of these organisms including both eukaryotes and prokaryotes has been constructed from the evolutionary distances (the rate of nucleotide substitution per site) data. The time of divergence of prokaryotes and eukaryotes was estimated to be greater than or congruent to 1.75x10(9) years ago and the branching order in eukaryotic kingdoms is consistent with the traditional order. Blue-green algae separated from the bacterial stem greater than or congruent to 1.3x10(9) years ago after eukaryotes had branched.

Sequence studies on the 5S RNA of Proteus vulgaris: comparison with 5S RNA of Escherichia coli

We have studied the sequence of 5S ribosomal RNA of Proteus vulgaris. Although several doubts remain, it seems that no more than 8 per cent of the nucleotides differ from those of Escherichia coli 5S RNA. Of the ten bases differing from Escherichia coli 5S RNA sequence, three changes take place in one of the six positions which are known as intercistronic mutation points in Escherichia coli 5S RNA. We can conclude that they are "hot spots" of mutation.

Nucleotide sequence of 5-S RNA from Bacillus licheniformis

The complete nucleotide sequence of 5-S RNA from Bacillus licheniformis was determined by analysis of complete and partial digests obtained with either T1 or pancreatic ribonuclease. The molecule was found to have a length of 116 nucleotides and may possess a minor sequence heterogeneity. There is a large degree of homology between the sequence of B. licheniformis 5-S RNA and those published for 5-S RNA from B. megatherium and B. stearothermophilus. The difference between the three 5-S RNA species are limited mainly to the two terminal and one internal sequence. B. licheniformis 5-S RNA contains the sequence U95-G-A-G-A-G100, which in B. subtilis has been implicated in the processing of precursor 5-S RNA. Possible models for the secondary structure of prokaryotic 5-S RNA are discussed on the basis of the results of limited digestion of B. licheniformis 5-S RNA by ribonuclease T1.

The architecture of 5S rRNA and its relation to function

An extensive comparative analysis of the available primary sequence data on 5S rRNA has been made. A universal secondary structure is presented for procaryotic 5S rRNA which contains four helical regions. Eucaryotic 5S rRNAs are found to have only three of these helices and thus have a somewhat different architecture. In addition, a highly conserved segment of more than thirty nucleotides is identified in the 5' half of the procaryotic molecule. This segment includes the oligonucleotide -CGAAC- which presumably binds to the t-RNA "common" sequence -GTpsiCG-. Among the eucaryotes, the plants display a procaryotic nature in this region, but no eucaryote has the sequence -CGAAC- in this segment. A functional role for the procaryotic 5S rRNA molecule is discussed in which it is envisioned to undergo conformational change, i.e., coiling and uncoiling of one of the helices, which can result in a cyclic interaction of the 5S rRNA molecule with two t-RNA molecules. A general principle also emerges: the natural rotational motion inherent in coiling and uncoiling of nucleic acid helices can be converted quite simply to linear mechanical motion.

The nucleotide sequence of the 5S ribosomal RNA from a photobacterium

Comparative sequencing studies provide powerful insights into molecular function and evolution. The sequence for 5S ribosomal RNA from Photobacter strain 8265 is eighteen base replacements removed from that of Escherichia coli. Of these, the vast majority involve a G or C becoming an A or U. These variations also define unequivocally a hexanucleotide base paired region, which appears to be a universal feature of the 5S RNA molecule. The base composition of this helix seems to be under rather stringent, and so unusual, energetic constraints. The possible implications of this are discussed - in particular the prospect of a 5S RNA molecule that undergoes conformational transitions as a part of the overall state changes that constitute the function of the ribosome.

Assembly of bacterial ribosomes

I have not mentioned the remarkable progress made mainly by Fellner and his co-workers (86) in the elucidation of the primary structure of rRNA's and by Wittmann and his co-workers (87) in determining the structure of several ribosomal proteins. Such knowledge of primary structures is certainly the basis of complete understanding of the structure of the ribosome. With the current progress in technology, complete elucidation of the primary structure of all the ribosomal components is probably a matter of time. As indicated in this article, a rough approximation of the three-dimensional structure of ribosomes is likely to emerge soon. Although not mentioned in this article, studies of ribosomes from higher organisms are also progressing. We must, therefore, consider what further studies should be conducted and what kinds of questions we would like to solve. Some groups of investigators aim to elucidate the complete three-dimensional structure of ribosomes and to find out how these complex cell organelles function; they hope to determine the conformational changes of many of the component molecules within the ribosome structure in response to external macromolecules and cofactors engaged in protein synthesis. Such knowledge will also be important in enabling us to understand the regulation of translation of genetic messages. Other groups of investigators aim to elucidate the complex series of events which originate in the transcription of the more than 60 genes and culminate in the formation of the specific structure of the organelle. Complete reproduction in vitro of all the assembly events that occur in vivo should not be difficult to achieve in principle. It should then become possible to study in vitro any factor regulating the biogenesis of the organelle. Although we do not know whether such studies would reveal any new fundamental principle that governs the complex circuits of interconnected macromolecular interactions, the achievement of such a complete in vitro system would represent a necessary step in the comprehensive understanding of biogenesis of organelles, and eventually, of the more complex behavior and genesis of cells (89).