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Caetano-Anollés G 《Nucleic acids research》2002,30(11):2575-2587
The elucidation of ribosomal structure has shown that the function of ribosomes is fundamentally confined to dynamic interactions established between the RNA components of the ribosomal ensemble. These findings now enable a detailed analysis of the evolution of ribosomal RNA (rRNA) structure. The origin and diversification of rRNA was studied here using phylogenetic tools directly at the structural level. A rooted universal tree was reconstructed from the combined secondary structures of large (LSU) and small (SSU) subunit rRNA using cladistic methods and considerations in statistical mechanics. The evolution of the complete repertoire of structural ribosomal characters was formally traced lineage-by-lineage in the tree, showing a tendency towards molecular simplification and a homogeneous reduction of ribosomal structural change with time. Character tracing revealed patterns of evolution in inter-subunit bridge contacts and tRNA-binding sites that were consistent with the proposed coupling of tRNA translocation and subunit movement. These patterns support the concerted evolution of tRNA-binding sites in the two subunits and the ancestral nature and common origin of certain structural ribosomal features, such as the peptidyl (P) site, the functional relay of the penultimate stem helix of SSU rRNA, and other structures participating in ribosomal dynamics. Overall results provide a rare insight into the evolution of ribosomal structure. 相似文献
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Secondary structure is evaluated for determining evolutionary relationships between catalytic RNA molecules that are so distantly
related they are scarcely alignable. The ribonucleoproteins RNase P (P) and RNase MRP (MRP) have been suggested to be evolutionarily
related because of similarities in both function and secondary structure. However, their RNA sequences cannot be aligned with
any confidence, and this leads to uncertainty in any trees inferred from sequences. We report several approaches to using
secondary structures for inferring evolutionary trees and emphasize quantitative tests to demonstrate that evolutionary information
can be recovered. For P and MRP, three hypotheses for the relatedness are considered. The first is that MRP is derived from
P in early eukaryotes. The next is that MRP is derived from P from an early endosymbiont. The third is that both P and MRP
evolved in the RNA-world (and the need for MRP has since been lost in prokaryotes). Quantitative comparisons of the pRNA and
mrpRNA secondary structures have found that the possibility of an organellar origin of MRP is unlikely. In addition, comparison
of secondary structures support the identity of an RNase P–like sequence in the maize chloroplast genome. Overall, it is concluded
that RNA secondary structure is useful for evaluating evolutionary relatedness, even with sequences that cannot be aligned
with confidence.
Received: 19 July 1999 / Accepted: 3 May 2000 相似文献
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5S rRNA is the smallest nucleic acid component of the large ribosomal subunit, contributing to ribosomal assembly, stability,
and function. Despite being a model for the study of RNA structure and RNA–protein interactions, the evolution of this universally
conserved molecule remains unclear. Here, we explore the history of the three-domain structure of 5S rRNA using phylogenetic
trees that are reconstructed directly from molecular structure. A total of 46 structural characters describing the geometry
of 666 5S rRNAs were used to derive intrinsically rooted trees of molecules and molecular substructures. Trees of molecules
revealed the tripartite nature of life. In these trees, superkingdom Archaea formed a paraphyletic basal group, while Bacteria
and Eukarya were monophyletic and derived. Trees of molecular substructures supported an origin of the molecule in a segment
that is homologous to helix I (α domain), its initial enhancement with helix III (β domain), and the early formation of the
three-domain structure typical of modern 5S rRNA in Archaea. The delayed formation of the branched structure in Bacteria and
Eukarya lends further support to the archaeal rooting of the tree of life. Remarkably, the evolution of molecular interactions
between 5S rRNA and associated ribosomal proteins inferred from a census of domain structure in hundreds of genomes established
a tight relationship between the age of 5S rRNA helices and the age of ribosomal proteins. Results suggest 5S rRNA originated
relatively quickly but quite late in evolution, at a time when primordial metabolic enzymes and translation machinery were
already in place. The molecule therefore represents a late evolutionary addition to the ribosomal ensemble that occurred prior
to the early diversification of Archaea. 相似文献
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In addition to characteristic structural properties imposed by evolutionary modification, evolved, single-stranded RNAs also
display characteristic structural properties imposed by intrinsic physical constraints on RNA polymer folding. The balance
of intrinsic and functionally selected characters in the folded conformation of evolved secondary structures was determined
by comparing the predicted secondary structures of evolved and unevolved (random) RNA sequences. Though evolved conformations
are significantly more ordered than conformations of random-sequence RNA, this analysis demonstrates that the majority of
conformational order within evolved structures results not from evolutionary optimization but from constraints imposed by
rules intrinsic to RNA polymer folding.
Received: 25 November 1998 / Accepted: 12 February 1999 相似文献
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We document the phylogenetic behavior of the 18S rRNA molecule in 67 taxa from 28 metazoan phyla and assess the effects of
among-site rate variation on reconstructing phylogenies of the animal kingdom. This empirical assessment was undertaken to
clarify further the limits of resolution of the 18S rRNA gene as a phylogenetic marker and to address the question of whether
18S rRNA phylogenies can be used as a source of evidence to infer the reality of a Cambrian explosion. A notable degree of
among-site rate variation exists between different regions of the 18S rRNA molecule, as well as within all classes of secondary
structure. There is a significant negative correlation between inferred number of nucleotide substitutions and phylogenetic
information, as well as with the degree of substitutional saturation within the molecule. Base compositional differences both
within and between taxa exist and, in certain lineages, may be associated with long branches and phylogenetic position. Importantly,
excluding sites with different degrees of nucleotide substitution significantly influences the topology and degree of resolution
of maximum-parsimony phylogenies as well as neighbor-joining phylogenies (corrected and uncorrected for among-site rate variation)
reconstructed at the metazoan scale. Together, these data indicate that the 18S rRNA molecule is an unsuitable candidate for
reconstructing the evolutionary history of all metazoan phyla, and that the polytomies, i.e., unresolved nodes within 18S
rRNA phylogenies, cannot be used as a single or reliable source of evidence to support the hypothesis of a Cambrian explosion.
Received: 9 December 1997 / Accepted: 23 March 1998 相似文献
7.
Novel strategies to study the role of mutation and nucleic acid structure in evolution 总被引:1,自引:0,他引:1
Natural selection processes tune genomes in the edge of the chaos imposed by mutation and drift, allowing an enduring exploration of fitter genetic networks within the constraints imposed by self-organization and the interactions of genotype and phenotype. Alternatively, evolution can be viewed from thermodynamic, kinetic or cybernetic perspectives. Regardless of insight, there is need to understand structure-function relationships at the molecular and holistic evolutionary levels. Strategies are here described that analyze genetic variation in time and trace the evolution of nucleic acid structure. Nucleic acid scanning techniques were used to measure sequence divergence and provide a direct inference of genome-wide mutation rate. This was tested for the first time in vegetatively propagating plants. The method is general and was also used in a study of mutational patterns in phytopathogenic fungi, showing there was a link between sequence and structural diversification of ribosomal gene spacers. In order to determine if this was a general phenomenon, the origin and diversification of nucleic acid secondary structure was traced using a cladistic method capable of producing rooted phylogenetic trees. Phylogenies reconstructed from primary and secondary RNA structure were congruent at all taxonomical levels, providing evidence of a strong link between phenotype and genotype favoring thermodynamic stability and dissipation of Gibbs free energy. Overall results suggest that thermodynamic principles are important driving forces of the evolutionary processes of the living world. 相似文献
8.
Two previously undetected domains were identified in a variety of RNA-binding proteins, particularly RNA-modifying enzymes,
using methods for sequence profile analysis. A small domain consisting of 60–65 amino acid residues was detected in the ribosomal
protein S4, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast protein containing
a pseudouridine synthetase and a deaminase domain, bacterial tyrosyl-tRNA synthetases, and a number of uncharacterized, small
proteins that may be involved in translation regulation. Another novel domain, designated PUA domain, after PseudoUridine
synthase and Archaeosine transglycosylase, was detected in archaeal and eukaryotic pseudouridine synthases, archaeal archaeosine
synthases, a family of predicted ATPases that may be involved in RNA modification, a family of predicted archaeal and bacterial
rRNA methylases. Additionally, the PUA domain was detected in a family of eukaryotic proteins that also contain a domain homologous
to the translation initiation factor eIF1/SUI1; these proteins may comprise a novel type of translation factors. Unexpectedly,
the PUA domain was detected also in bacterial and yeast glutamate kinases; this is compatible with the demonstrated role of
these enzymes in the regulation of the expression of other genes. We propose that the S4 domain and the PUA domain bind RNA
molecules with complex folded structures, adding to the growing collection of nucleic acid-binding domains associated with
DNA and RNA modification enzymes. The evolution of the translation machinery components containing the S4, PUA, and SUI1 domains
must have included several events of lateral gene transfer and gene loss as well as lineage-specific domain fusions.
Received: 15 May 1998 / Accepted: 20 July 1998 相似文献
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Miyuki Noro Ryuichi Masuda Irena A. Dubrovo Michihiro C. Yoshida Makoto Kato 《Journal of molecular evolution》1998,46(3):314-326
Complete sequences of cytochrome b (1,137 bases) and 12S ribosomal RNA (961 bases) genes in mitochondrial DNA were successfully determined from the woolly mammoth
(Mammuthus primigenius), African elephant (Loxodonta africana), and Asian elephant (Elephas maximus). From these sequence data, phylogenetic relationships among three genera were examined. Molecular phylogenetic trees reconstructed
by the neighbor-joining and the maximum parsimony methods provided an identical topology both for cytochrome b and 12S rRNA genes. These results support the ``Mammuthus-Loxodonta' clade, which is contrary to some previous morphological reports that Mammuthus is more closely related to Elephas than to Loxodonta.
Received: 8 April 1997 / Accepted: 23 July 1997 相似文献
11.
Thomas Cavalier-Smith 《Journal of molecular evolution》2001,53(4-5):555-595
I attempt to sketch a unified picture of the origin of living organisms in their genetic, bioenergetic, and structural aspects.
Only selection at a higher level than for individual selfish genes could power the cooperative macromolecular coevolution
required for evolving the genetic code. The protein synthesis machinery is too complex to have evolved before membranes. Therefore
a symbiosis of membranes, replicators, and catalysts probably mediated the origin of the code and the transition from a nucleic
acid world of independent molecular replicators to a nucleic acid/protein/lipid world of reproducing organisms. Membranes
initially functioned as supramolecular structures to which different replicators attached and were selected as a higher-level
reproductive unit: the proto-organism. I discuss the roles of stereochemistry, gene divergence, codon capture, and selection
in the code's origin. I argue that proteins were primarily structural not enzymatic and that the first biological membranes
consisted of amphipathic peptidyl-tRNAs and prebiotic mixed lipids. The peptidyl-tRNAs functioned as genetically-specified
lipid analogues with hydrophobic tails (ancestral signal peptides) and hydrophilic polynucleotide heads. Protoribosomes arose
from two cooperating RNAs: peptidyl transferase (large subunit) and mRNA-binder (small subunit). Early proteins had a second
key role: coupling energy flow to the phosphorylation of gene and peptide precursors, probably by lithophosphorylation by
membrane-anchored kinases scavenging geothermal polyphosphate stocks. These key evolutionary steps probably occurred on the
outer surface of an `inside out-cell' or obcell, which evolved an unambiguous hydrophobic code with four prebiotic amino acids
and proline, and initiation by isoleucine anticodon CAU; early proteins and nucleozymes were all membrane-attached. To improve
replication, translation, and lithophosphorylation, hydrophilic substrate-binding and catalytic domains were later added to
signal peptides, yielding a ten-acid doublet code. A primitive proto-ecology of molecular scavenging, parasitism, and predation
evolved among obcells. I propose a new theory for the origin of the first cell: fusion of two cup-shaped obcells, or hemicells,
to make a protocell with double envelope, internal genome and ribosomes, protocytosol, and periplasm. Only then did water-soluble
enzymes, amino acid biosynthesis, and intermediary metabolism evolve in a concentrated autocatalytic internal cytosolic soup,
causing 12 new amino acid assignments, termination, and rapid freezing of the 22-acid code. Anticodons were recruited sequentially:
GNN, CNN, INN, and *UNN. CO2 fixation, photoreduction, and lipid synthesis probably evolved in the protocell before photophosphorylation. Signal recognition
particles, chaperones, compartmented proteases, and peptidoglycan arose prior to the last common ancestor of life, a complex
autotrophic, anaerobic green bacterium.
Received: 19 February 2001 / Accepted: 9 April 2001 相似文献
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Although molecular phylogenetic studies of cyanobacteria on the basis of the 16S rRNA gene sequence have been reported, the
topologies were unstable, especially in the inner branchings. Our analysis of 16S rRNA gene phylogeny by the maximum-likelihood
and neighbor-joining methods combined with rate homogeneous and heterogeneous models revealed seven major evolutionary lineages
of the cyanobacteria, including prochlorophycean organisms. These seven lineages are always stable on any combination of these
methods and models, fundamentally corresponding to phylogenetic relationships based on other genes, e.g., psbA, rbcL, rnpB, rpoC, and tufA. Moreover, although known genotypic and phenotypic characters sometimes appear paralleled in independent lineages, many characters
are not contradictory within each group. Therefore we propose seven evolutionary groups as a working hypothesis for successive
taxonomic reconstruction. New 16S rRNA sequences of five unicellular cyanobacterial strains, PCC 7001, PCC 7003, PCC 73109,
PCC 7117, and PCC 7335 of Synechococcus sp., were determined in this study. Although all these strains have been assigned to ``marine clusters B and C,' they were
separated into three lineages. This suggests that the organisms classified in the genus Synechococcus evolved diversely and should be reclassified in several independent taxonomic units. Moreover, Synechococcus strains and filamentous cyanobacteria make a monophyletic group supported by a comparatively high statistical confidence
value (80 to 100%) in each of the two independent lineages; therefore, these monophylies probably reflect the convergent evolution
of a multicellular organization.
Received: 3 September 1998 / Accepted: 30 November 1998 相似文献
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The secondary structure of rRNA internal transcribed spacer 2 is important in the process of ribosomal biogenesis. Trematode
ITS sequences are poorly conserved and difficult to align for phylogenetic comparisons above a family level. If a conserved
secondary structure can be identified, it can be used to guide primary sequence alignments. ITS2 sequences from 39 species
were compared. These species span four orders of trematodes (Echinostomiformes, Plagiorchiformes, Strigeiformes, and Paramphistomiformes)
and one monogenean (Gyrodactyliformes). The sequences vary in length from 251 to 431 bases, with an average GC content of
48%. The monogenean sequence could not be aligned with confidence to the trematodes. Above the family level trematode sequences
were alignable from the 5′ end for 139 bases. Secondary structure foldings predicted a four-domain model. Three folding patterns
were required for the apex of domain B. The folding pattern of domains C and D varies for each family. The structures display
a high GC content within stems. Bases A and U are favored in unpaired regions and variable sites cluster. This produces a
mosaic of conserved and variable regions with a structural conformation resistant to change. Two conserved strings were identified,
one in domain B and the other in domain C. The first site can be aligned to a processing site identified in yeast and rat.
The second site has been found in plants, and structural location appears to be important. A phylogenetic tree of the trematode
sequences, aligned with the aid of secondary structures, distinguishes the four recognized orders.
Received: 21 November 1997 / Accepted: 9 February 1998 相似文献
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J. Robert Macey Allan Larson Natalia B. Ananjeva Theodore J. Papenfuss 《Journal of molecular evolution》1997,44(6):660-674
A phylogenetic tree for major lineages of iguanian lizards is estimated from 1,488 aligned base positions (858 informative)
of newly reported mitochondrial DNA sequences representing coding regions for eight tRNAs, ND2, and portions of ND1 and COI.
Two well-supported groups are defined, the Acrodonta and the Iguanidae (sensu lato). This phylogenetic hypothesis is used
to investigate evolutionary shifts in mitochondrial gene order, origin for light-strand replication, and secondary structure
of tRNACys. These three characters shift together on the branch leading to acrodont lizards. Plate tectonics and the fossil record indicate
that these characters changed in the Jurassic. We propose that changes to the secondary structure of tRNACys may destroy function of the origin for light-strand replication which, in turn, may facilitate shifts in gene order.
Received: 28 May 1996 / Accepted: 27 December 1996 相似文献
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Relics from the RNA World 总被引:1,自引:0,他引:1
An RNA world is widely accepted as a probable stage in the early evolution of life. Two implications are that proteins have
gradually replaced RNA as the main biological catalysts and that RNA has not taken on any major de novo catalytic function
after the evolution of protein synthesis, that is, there is an essentially irreversible series of steps RNA → RNP → protein.
This transition, as expected from a consideration of catalytic perfection, is essentially complete for reactions when the
substrates are small molecules. Based on these principles we derive criteria for identifying RNAs in modern organisms that
are relics from the RNA world and then examine the function and phylogenetic distribution of RNA for such remnants of the
RNA world. This allows an estimate of the minimum complexity of the last ribo-organism—the stage just preceding the advent
of genetically encoded protein synthesis. Despite the constraints placed on its size by a low fidelity of replication (the
Eigen limit), we conclude that the genome of this organism reached a considerable level of complexity that included several
RNA-processing steps. It would include a large protoribosome with many smaller RNAs involved in its assembly, pre-tRNAs and
tRNA processing, an ability for recombination of RNA, some RNA editing, an ability to copy to the end of each RNA strand,
and some transport functions. It is harder to recognize specific metabolic reactions that must have existed but synthetic
and bio-energetic functions would be necessary. Overall, this requires that such an organism maintained a multiple copy, double-stranded
linear RNA genome capable of recombination and splicing. The genome was most likely fragmented, allowing each ``chromosome'
to be replicated with minimum error, that is, within the Eigen limit. The model as developed serves as an outgroup to root
the tree of life and is an alternative to using sequence data for inferring properties of the earliest cells.
Received: 14 January 1997 / Accepted: 19 May 1997 相似文献
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Molecular Data from the 16S rRNA Gene for the Phylogeny of Pectinidae (Mollusca: Bivalvia) 总被引:17,自引:0,他引:17
The phylogenetic relationships among the species belonging to the family Pectinidae are still an issue of debate. The mitochondrial
DNA sequences from the large ribosomal RNA gene may be of great value for systematic and phylogenetic studies within families.
Partial sequences of the 16S rRNA gene were obtained for the scallop species Adamussium colbecki, Aequipecten opercularis, Chlamys glabra, C. islandica, C. varia, and Pecten jacobeus and compared with the published sequence of Pecten maximus. The present molecular data show that Chlamys are polyphyletic and do not support the assignment of these species to the two subfamilies Chlamydinae and Pectininae. Moreover,
the minimal genetic distance between P. maximus and P. jacobeus suggests that they could belong to the same species.
Received: 24 May 1999 / Accepted: 1 September 1999 相似文献
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rRNA二级结构序列用于真菌系统学研究的方法初探 总被引:1,自引:0,他引:1
本文首次利用核酸二级结构特征代替核酸碱基作为探讨类群之间亲缘关系的信号,构建了基于结构特征的子囊菌部分类群的系统进化树。该方法以S(规范的碱基对),Q(不规范的碱基对),I(单链),B(侧环),M(多分枝环)和H(发卡结构)为代码将二级结构特征区分为6种不同的亚结构类型,然后将二级结构特征转换为结构序列,并进行结构序列分析。该方法使rRNA不只局限于碱基比较,拓展了其应用范围,为揭示分子的功能与进化的关系提供了线索。结果表明,结构序列分析可用于子囊菌的系统学研究;相对于核酸序列分析,结构分析的结果似乎更加清晰地体现子囊果的演化过程。 相似文献
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The primary and secondary structure of the small-subunit ribosomal RNA (ssrRNA) gene from the naked, marine amoeba, Vannella anglica (subclass Gymnamoebia), was determined. The ssrRNA is 1962 nucleotides in length, with a low G+C content of 37.1%. The ssrRNA
is composed of several uncommon secondary structure features including helix E8-1, which may be a useful target for rRNA probes
for the direct identification of isolates in mixed culture. Phylogenetic analysis of sequence data showed that V. anglica branched prior to the rapid diversification of the eukaryotes. It did not associate with the other naked, lobose amoebae
represented by Acanthamoeba and Hartmannella, indicating that Vannella represents a separate amoeboid lineage and the subclass Gymnamoebia is polyphyletic.
Received: 9 July 1998 / Accepted: 16 November 1998 相似文献