A phylogenetic analysis based upon ribosomal RNA sequence characterization reveals that living systems represent one of three aboriginal lines of descent: (i) the eubacteria, comprising all typical bacteria; (ii) the archaebacteria, containing methanogenic bacteria; and (iii) the urkaryotes, now represented in the cytoplasmic component of eukaryotic cells. The biologist has customarily structured his world in terms of certain basic dichotomies. Classically, what was not plant was animal. The discovery that bacteria, which initially had been considered plants, resembled both plants and animals less than plants and animals resembled one another led to a reformulation of the issue in terms of a yet more basic dichotomy, that of eukaryote versus prokaryote. The striking differences between eukaryotic and prokaryotic cells have now been documented in endless molecular detail. As a result, it is generally taken for granted that all extant life must be of these two basic types.Thus, it appears that the biologist has solved the problem of the primary phylogenetic groupings. However, this is not the case. Dividing the living world into Prokaryotae and Eukaryotae has served, if anything, to obscure the problem of what extant groupings represent the various primeval branches from the common line of descent. The reason is that eukaryote/ prokaryote is not primarily a phylogenetic distinction, although it is generally treated so. The eukaryotic cell is organized in a different and more complex way than is the prokaryote; this probably reflects the former's composite origin as a symbiotic collection of various simpler organisms (1-5). However striking, these organizational dissimilarities do not guarantee that eukaryote and prokaryote represent phylogenetic extremes.The eukaryotic cell per se cannot be directly compared to the prokaryote. The composite nature of the eukaryotic cell makes it necessary that it first be conceptually reduced to its phylogenetically separate components, which arose from ancestors that were noncomposite and so individually are comparable to prokaryotes. In other words, the question of the primary phylogenetic groupings must be formulated solely in terms of relationships among "prokaryotes"-i.e., noncomposite entities. (Note that in this context there is no suggestion a priori that the living world is structured in a dichotomous way.)The organizational differences between prokaryote and eukaryote and the composite nature of the latter indicate an important property of the evolutionary process: Evolution seems to progress in a "quantized" fashion. One level or domain of organization gives rise ultimately to a higher (more complex) one. What "prokaryote" and "eukaryote" actually represent are two such domains. Thus, although it is useful to define phylogenetic patterns within each domain, it is not meaningful The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 U. S. ...

16s rRNA (genes coding for rRNA) sequence comparisons were conducted with the following three psychrophilic strains: Bacillus globisporus W25* (T = type strain) and Bacillus psychrophilus W16AT, and W5.These strains exhibited more than 99.5 % sequence identity and within experimental uncertainty could be regarded as identical. Their close taxonomic relationship was further documented by phenotypic similarities. In contrast, previously published DNA-DNA hybridization results have convincingly established that these strains do not belong to the same species if current standards are used. These results emphasize the important point that effective identity of 16s rRNA sequences is not necessarily a sufficient criterion to guarantee species identity. Thus, although 16s rRNA sequences can be used routinely to distinguish and establish relationships between genera and well-resolved species, very recently diverged species may not be recognizable.

We present a molecular-level model for the origin and evolution of the translation system, using a 3D comparative method. In this model, the ribosome evolved by accretion, recursively adding expansion segments, iteratively growing, subsuming, and freezing the rRNA. Functions of expansion segments in the ancestral ribosome are assigned by correspondence with their functions in the extant ribosome. The model explains the evolution of the large ribosomal subunit, the small ribosomal subunit, tRNA, and mRNA. Prokaryotic ribosomes evolved in six phases, sequentially acquiring capabilities for RNA folding, catalysis, subunit association, correlated evolution, decoding, energy-driven translocation, and surface proteinization. Two additional phases exclusive to eukaryotes led to tentacle-like rRNA expansions. In this model, ribosomal proteinization was a driving force for the broad adoption of proteins in other biological processes. The exit tunnel was clearly a central theme of all phases of ribosomal evolution and was continuously extended and rigidified. In the primitive noncoding ribosome, proto-mRNA and the small ribosomal subunit acted as cofactors, positioning the activated ends of tRNAs within the peptidyl transferase center. This association linked the evolution of the large and small ribosomal subunits, protomRNA, and tRNA.RNA evolution | translation | origin of life | A-minor interactions T he ribosome retains interpretable molecular records of a world of primordial molecules (1) from around 4 billion years ago (2-9). The records are maintained in rRNA secondary and 3D structures, which are fully conserved throughout the tree of life, and in rRNA sequences, which are more variable (SI Appendix, Fig. S1). Here we use information within ribosomes from each major branch of the tree of life to reconstruct much of the emergence of the universal translational machinery. Large Ribosomal Subunit EvolutionPreviously, we reported a 3D comparative method that revealed a molecular level chronology of the evolution of the large ribosomal subunit (LSU) rRNA (10). Insertion fingerprints are evident when comparing 3D structures of LSU rRNAs of various sizes from various species. These insertion fingerprints mark sites where rRNA expands, recording growth steps on a molecular level.Within the common core of the LSU rRNA, insertion fingerprints were used to identify ancient growth sites. We showed that insertion fingerprints provide a roadmap from the first steps in the formation of the peptidyl transferase center (PTC) (10) located in the ancient heart of the LSU (2-6), culminating in the common core.Small Ribosomal Subunit, LSU, tRNA, and mRNA Evolution Here, using the 3D comparative method, we establish a comprehensive and coherent model for the evolution of the entire ribosome. This model covers the LSU rRNA, small ribosomal subunit (SSU) rRNA, tRNA, and mRNA. The evolution of each of these components is reconciled at the molecular level to a common chronology. This evolutionary model, which we call the "accretion model," ...

The origins and evolution of the ribosome, 3-4 billion years ago, remain imprinted in the biochemistry of extant life and in the structure of the ribosome. Processes of ribosomal RNA (rRNA) expansion can be "observed" by comparing 3D rRNA structures of bacteria (small), yeast (medium), and metazoans (large). rRNA size correlates well with species complexity. Differences in ribosomes across species reveal that rRNA expansion segments have been added to rRNAs without perturbing the preexisting core. Here we show that rRNA growth occurs by a limited number of processes that include inserting a branch helix onto a preexisting trunk helix and elongation of a helix. rRNA expansions can leave distinctive atomic resolution fingerprints, which we call "insertion fingerprints." Observation of insertion fingerprints in the ribosomal common core allows identification of probable ancestral expansion segments. Conceptually reversing these expansions allows extrapolation backward in time to generate models of primordial ribosomes. The approach presented here provides insight to the structure of pre-last universal common ancestor rRNAs and the subsequent expansions that shaped the peptidyl transferase center and the conserved core. We infer distinct phases of ribosomal evolution through which ribosomal particles evolve, acquiring coding and translocation, and extending and elaborating the exit tunnel.RNA evolution | C value | origin of life | translation | phylogeny T he translation system, one of life's universal processes, synthesizes all coded protein in living systems. Our understanding of translation has advanced over the last decade and a half with the explosion in sequencing data and by the determination of 3D structures (1-4). X-ray crystallography and cryoelectron microscopy (cryo-EM) have provided atomic resolution structures of ribosomes from all three domains of life. Eukaryotic ribosomal structures are now available from protists (5), fungi (6), plants (7), insects, and humans (8). Here we describe an atomic level model of the evolution of ribosomal RNA (rRNA) from the large ribosomal subunit (LSU). Our evolutionary model is grounded in patterns of rRNA growth in relatively recent ribosomal expansions, for which there is an extensive, atomicresolution record.The common core LSU rRNA (9, 10), which is approximated here by the rRNA of Escherichia coli, is conserved over the entire phylogenetic tree, in sequence, and especially in secondary structure (11) and 3D structure (12). By contrast, the surface regions and the sizes of ribosomes are variable (13,14). Most of the size variability is found in eukaryotic LSUs (Fig. 1). The integrated rRNA size in the LSU follows the trend Bacteria ≤ Archaea < Eukarya. The added rRNA in eukaryotes interacts with eukaryotic-specific proteins (5, 8, 9) (SI Appendix, Fig. S1 and Dataset S1).Bacterial and archaeal LSU rRNAs are composed entirely of the common core, with only subtle deviations from it. By contrast, eukaryotic LSU rRNAs are expanded beyond the common core. Sacccharomyce...