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1.
2.
In translation, separate aminoacyl-tRNA synthetases attach the 20 different amino acids to their cognate tRNAs, with the
exception of glutamine. Eukaryotes and some bacteria employ a specific glutaminyl-tRNA synthetase (GlnRS) which other Bacteria,
the Archaea (archaebacteria), and organelles apparently lack. Instead, tRNAGln is initially acylated with glutamate by glutamyl-tRNA synthetase (GluRS), then the glutamate moiety is transamidated to glutamine.
Lamour et al. [(1994) Proc Natl Acad Sci USA 91:8670–8674] suggested that an early duplication of the GluRS gene in eukaryotes
gave rise to the gene for GlnRS—a copy of which was subsequently transferred to proteobacteria. However, questions remain
about the occurrence of GlnRS genes among the Eucarya (eukaryotes) outside of the ``crown' taxa (animals, fungi, and plants),
the distribution of GlnRS genes in the Bacteria, and their evolutionary relationships to genes from the Archaea. Here, we
show that GlnRS occurs in the most deeply branching eukaryotes and that putative GluRS genes from the Archaea are more closely
related to GlnRS and GluRS genes of the Eucarya than to those of Bacteria. There is still no evidence for the existence of
GlnRS in the Archaea. We propose that the last common ancestor to contemporary cells, or cenancestor, used transamidation
to synthesize Gln-tRNAGln and that both the Bacteria and the Archaea retained this pathway, while eukaryotes developed a specific GlnRS gene through
the duplication of an existing GluRS gene. In the Bacteria, GlnRS genes have been identified in a total of 10 species from
three highly diverse taxonomic groups: Thermus/Deinococcus, Proteobacteria γ/β subdivision, and Bacteroides/Cytophaga/Flexibacter.
Although all bacterial GlnRS form a monophyletic group, the broad phyletic distribution of this tRNA synthetase suggests that
multiple gene transfers from eukaryotes to bacteria occurred shortly after the Archaea–eukaryote divergence. 相似文献
3.
We present a novel hypothesis for the origin of the eukaryotic cell, or eukaryogenesis, based on a metabolic symbiosis (syntrophy)
between a methanogenic archaeon (methanobacterial-like) and a δ-proteobacterium (an ancestral sulfate-reducing myxobacterium).
This syntrophic symbiosis was originally mediated by interspecies H2 transfer in anaerobic, possibly moderately thermophilic, environments. During eukaryogenesis, progressive cellular and genomic
cointegration of both types of prokaryotic partners occurred. Initially, the establishment of permanent consortia, accompanied
by extensive membrane development and close cell–cell interactions, led to a highly evolved symbiotic structure already endowed
with some primitive eukaryotic features, such as a complex membrane system defining a protonuclear space (corresponding to
the archaeal cytoplasm), and a protoplasmic region (derived from fusion of the surrounding bacterial cells). Simultaneously,
bacterial-to-archaeal preferential gene transfer and eventual replacement took place. Bacterial genome extinction was thus
accomplished by gradual transfer to the archaeal host, where genes adapted to a new genetic environment. Emerging eukaryotes
would have inherited archaeal genome organization and dynamics and, consequently, most DNA-processing information systems.
Conversely, primordial genes for social and developmental behavior would have been provided by the ancient myxobacterial symbiont.
Metabolism would have been issued mainly from the versatile bacterial organotrophy, and progressively, methanogenesis was
lost.
Received: 5 January 1998 / Accepted: 18 March 1998 相似文献
4.
We inferred the incidence of nucleotide conversions in the COI and 16S rRNA mitochondrial genes of members of the Symphyta
and basal Apocrita (Hymenoptera). Character-state reconstructions in both genes suggested that conversions between A and T
(AT transversions) occurred much more frequently than any other type of change, although we cannot wholly discount an underlying
transition bias. Parsimony analysis of COI nucleotide characters did not recover phylogeny; e.g., neither the Tenthredinoidea
nor Apocrita were recovered as monophyletic. However, analysis of COI amino acid characters did recover these relationships,
as well as others based on fossil and morphological evidence. Analysis of 16S rRNA characters also recovered these relationships
providing conversions between A and T were down-weighted. Analysis of the combined data sets gave relatively strong support
for various relationships, suggesting that both data sets supported similar topographies. These data sets, both separately
and combined, suggested that the phytophagous Siricidae were more closely related to the predominantly parasitic Apocrita
than were the ectoparasitic Orussoidea. This suggests that the wasp parasitic lifestyle did not have a single origin, unless
the Siricidae have more recently reverted to phytophagy. Alternatively, parasitism evolved twice independently, once in the
Orussoidea and again in the Apocrita. The latter scenario is supported by the observation that the evolution of parasitism
was accompanied by a tendency for the larvae to develop inside plant tissues. Adaptations that accompanied the movement of
wasps into a confined, wood-boring habitat may have preadapted them to becoming ectoparasitic.
Received: 27 March 1996 / Accepted: 2 August 1996 相似文献
5.
Radu Popa 《Journal of molecular evolution》1997,44(2):121-127
A sequential model is proposed regarding the origin of biological chirality. Three major stages are presumed: a symmetry
breaking (prebiotic chiral disruption in enantiomeric mixtures of monomers), a chiral amplification (prebiotic increase of
the chiral character of the monomers affected first by the symmetry breaking), and a chiral expansion (proto biological increase
of the chiral character and spread of the chirality to molecules which were less affected by prebiotic chiralizations). As
a symmetry-breaking mechanism, the model proposed by Deutsch (1991) is used, which involves a dissymmetric exposure of amino
acids (AA) to ultraviolet circularly polarized light (UV-CPL) on evaporative seashores. It is presumed that the chiral amplification,
up to a protobiologic significance, was influenced by a periodic overlapping of two abiotic events, a synchronization between
tidal-based hydrous–anhydrous cycles, and littoral asymmetric photolysis cycles. This long-term astronomic asymmetry acted
around 3.8–4.2 billion years ago and was unique to the Earth in our solar system. It is also presumed that the abiotic symmetry
breaking is heterogenous, that only a few l-AAs were used in the beginning, and that the chirality expanded later to all 20 AAs based on a coevolutionary strategy of
the genetic code and on a physiological relationship between AAs. In this scenario the d-chirality of pentoses in polynucleotides was attributed to both d-pentose/l-AA relationships and to a structural evolution.
Received: 10 May 1996 / Accepted: 13 August 1996 相似文献
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7.
A comprehensive evolutionary analysis of aquaporins, a family of intrinsic membrane proteins that function as water channels, was conducted to establish groups of homology (i.e., to identify orthologues and paralogues) within the family and to gain insights into the functional constraints acting on the structure of the aquaporin molecule structure. Aquaporins are present in all living organisms, and therefore, they provide an excellent opportunity to further our understanding of the broader biological significance of molecular evolution by gene duplication followed by functional and structural specialization. Based on the resulting phylogeny, the 153 channel proteins analyzed were classified into six major paralogous groups: (1) GLPs, or glycerol-transporting channel proteins, which include mammalian AQP3, AQP7, and AQP9, several nematode paralogues, a yeast paralogue, and Escherichia coli GLP; (2) AQPs, or aquaporins, which include metazoan AQP0, AQP1, AQP2, AQP4, AQP5, and AQP6; (3) PIPs, or plasma membrane intrinsic proteins of plants, which include PIP1 and PIP2; (4) TIPs, or tonoplast intrinsic proteins of plants, which include alphaTIP, gammaTIP, and deltaTIP; (5) NODs, or nodulins of plants; and (6) AQP8s, or metazoan aquaporin 8 proteins. Of these groups, AQPs, PIPs, and TIPs cluster together. According to the results, the capacity to transport glycerol shown by several members of the family was acquired only early in the history of the family. The new phylogeny reveals that several water channel proteins are misclassified and require reassignment, whereas several previously undetermined ones can now be classified with confidence. The deduced phylogenetic framework was used to characterize the molecular features of water channel proteins. Three motifs are common to all family members: AEF (Ala-Glu-Phe), which is located in the N-terminal domain; and two NPA (Asp-Pro-Ala) boxes, which are located in the center and C-terminal domains, respectively. Other residues are found to be conserved within the major groups but not among them. Overall, the PIP subfamily showed the least variation. In general, no radical amino acid replacements affecting tertiary structure were identified, with the exception of Ala-->Ser in the TIP subfamily. Constancy of rates of evolution was demonstrated within the different paralogues but rejected among several of them (GLP and NOD). 相似文献
8.
Aurora M. Nedelcu 《Journal of molecular evolution》2001,53(6):670-679
This study provides a phylogenetic/comparative approach to deciphering the processes underlying the evolution of plastid
rRNA genes in genomes under relaxed functional constraints. Nonphotosynthetic green algal taxa that belong to two distinct
classes, Chlorophyceae (Polytoma) and Trebouxiophyceae (Prototheca), were investigated. Similar to the situation described previously for plastid 16S rRNA genes in nonphotosynthetic land plants,
nucleotide substitution levels, extent of structural variations, and percentage AT values are increased in nonphotosynthetic
green algae compared to their closest photosynthetic relatives. However, the mutational processes appear to be different in
many respects. First, with the increase in AT content, more transversions are noted in Polytoma and holoparasite angiosperms, while more transitions characterize the evolution of the 16S rDNA sequences in Prototheca. Second, although structural variations do accumulate in both Polytoma and Prototheca (as well as holoparasitic plastid 16S rRNAs), insertions as large as 1.6 kb characterize the plastid 16S rRNA genes in the
former, whereas significantly smaller indels (not exceeding 24 bp) seem to be more prevalent in the latter group. The differences
in evolutionary rates and patterns within and between lineages might be due to mutations in replication/repair-related genes;
slipped-strand mispairing is likely the mechanism responsible for the expansion of insertions in Polytoma plastid 16S rRNA genes.
Received: 29 December 2000 / Accepted: 18 May 2001 相似文献
9.
Shneior Lifson 《Journal of molecular evolution》1997,44(1):1-8
Theories of the origin of life have proposed hypotheses to link inanimate to animate matter. The theory proposed here derived
the crucial stages in the origin of animate matter directly from the basic properties of inanimate matter. It asked what were
the general characteristics of the link, rather than what might have been its chemical details. Life and its origin are shown to be one continuous physicochemical process of replication, random variation, and natural
selection. Since life exists here and now, animate properties must have been initiated in the past somewhere. According to
the theory, life originated from an as yet unknown elementary autocatalyst which occurred spontaneously, then replicated autocatalytically. As it multiplied to macroscopic abundance, its replicas
gradually exhausted their reactants. Random chemical drift initiated diversity among autocatalysts. Diversity led to competition. Competition and depletion of reactants slowed down the rates of net replication
of the autocatalysts. Some reached negative rates and became extinct, while those which stayed positive ``survived.' Thus
chemical natural selection appeared, the first step in the transition from inanimate to animate matter. It initiated the first animate property, fitness, i.e., the capacity to adapt to the environment and to survive. As the environment was depleted of reactants, it was enriched with sequels—namely, with decomposition products and all other products which accompany autocatalysis. The changing environment exerted
a selective pressure on autocatalysts to replace dwindling reactants by accumulating sequels. Sequels that were incorporated
into the autocatalytic process became internal components of complex autocatalytic systems. Primitive forms of metabolism and organization were thus initiated. They evolved further by the same mechanism to ever higher levels of complexity, such
as homochirality (handedness) and membranal enclosure. Subsequent evolution by the same mechanism generated cellular metabolism,
cell division, information carriers, and a genetic code. Theories of self-organization without natural selection are refuted.
Received: 29 March 1996 / Accepted: 30 May 1996 相似文献
10.
A new method for looking at relationships between nucleotide sequences has been used to analyze divergence both within and
between the families of isoaccepting tRNA sets. A dendrogram of the relationships between 21 tRNA sets with different amino
acid specificities is presented as the result of the analysis. Methionine initiator tRNAs are included as a separate set.
The dendrogram has been interpreted with respect to the final stage of the evolutionary pathway with the development of highly
specific tRNAs from ambiguous molecular adaptors. The location of the sets on the dendrogram was therefore analyzed in relation
to hypotheses on the origin of the genetic code: the coevolution theory, the physicochemical hypothesis, and the hypothesis
of ambiguity reduction of the genetic code. Pairs of 16 sets of isoacceptor tRNAs, whose amino acids are in biosynthetic relationships,
occupied contiguous positions on the dendrogram, thus supporting the coevolution theory of the genetic code.
Received: 4 May 1998 / Accepted: 11 July 1998 相似文献
11.
Herdman M Coursin T Rippka R Houmard J Tandeau de Marsac N 《Journal of molecular evolution》2000,51(3):205-213
The evolutionary origin of the phytochromes of eukaryotes is controversial. Three cyanobacterial proteins have been described
as ``phytochrome-like' and have been suggested to be potential ancestors of these essential photoreceptors: Cph1 from Synechocystis PCC 6803, showing homology to phytochromes along its entire length and known to attach a chromophore; and PlpA from Synechocystis PCC 6803 and RcaE from Fremyella diplosiphon, both showing homology to phytochromes most strongly only in the C-terminal region and not known to bind a chromophore. We
have reexamined the evolution of the photoreceptors using for PCR amplification a highly conserved region encoding the chromophore-binding
domain in both Cph1 and phytochromes of plants and have identified genes for phytochrome-like proteins (PLP) in 11 very diverse
cyanobacteria. The predicted gene products contain either a Cys, Arg, Ile, or Leu residue at the putative chromophore binding
site. In 10 of the strains examined only a single gene was found, but in Calothrix PCC 7601 two genes (cphA and cphB) were identified. Phylogenetic analysis revealed that genes encoding PLP are homologues that share a common ancestor with
the phytochromes of eukaryotes and diverged before the latter. In contrast, the putative sensory/regulatory proteins, including
PlpA and RcaE, that lack a part of the chromophore lyase domain essential for chromophore attachment on the apophytochrome,
are only distantly related to phytochromes. The Ppr protein of the anoxygenic photosynthetic bacterium Rhodospirillum centenum and the bacterial phytochrome-like proteins (BphP) of Deinococcus radiodurans and Pseudomonas aeruginosa fall within the cluster of cyanobacterial phytochromes.
Received: 9 December 1999 / Accepted: 10 May 2000 相似文献
12.
Analysis of the 18S rDNA sequences of five species of the family Dugesiidae (phylum Platyhelminthes, suborder Tricladida,
infraorder Paludicola) and eight species belonging to families Dendrocoelidae and Planaridae and to the infraorder Maricola
showed that members of the family Dugesiidae have two types of 18S rDNA genes, while the rest of the species have only one.
The duplication event also affected the ITS-1, 5.8S, ITS-2 region and probably the 28S gene. The mean divergence value between
the type I and the type II sequences is 9% and type II 18S rDNA genes are evolving 2.3 times more rapidly than type I. The
evolutionary rates of type I and type II genes were calibrated from biogeographical data, and an approximate date for the
duplication event of 80–120 million years ago was calculated. The type II gene was shown, by RT-PCR, to be transcribed in
adult individuals of Schmidtea polychroa, though at very low levels. This result, together with the fact that most of the functionally important positions for small-subunit
rRNA in prokaryotes have been conserved, indicates that the type II gene is probably functional.
Received: 24 March 1998 / Accepted: 17 March 1999 相似文献
13.
Satoshi Yamagishi Masanao Honda Kazuhiro Eguchi Russel Thorstrom 《Journal of molecular evolution》2001,53(1):39-46
Phylogenetic relationships of the family Vangidae and representatives of several other passeriform families were inferred
from 882 base positions of mitochondrial DNA sequences of 12S and 16S rRNA genes. Results indicated the monophyly of the Vangidae,
which includes the genus Tylas, hitherto often placed in the family Pycnonotidae. Our results also revealed the Malagasy endemic Newtonia, a genus never previously assigned to the Vangidae, to be a member of this family. These results suggest the occurrence of
an extensive in situ radiation of this family within Madagascar, and that the extant high diversity of this family is not the result of multiple
colonizations from outside. The extremely high morphological and ecological diversification of the family seems to have been
enhanced through the use and ultimate occupancy of vacant niches in this island.
Received: 8 September 2000 / Accepted: 13 February 2001 相似文献
14.
Héctor Musto Héctor Romero Alejandro Zavala Giorgio Bernardi 《Journal of molecular evolution》1999,49(3):325-329
This paper analyses the compositional correlations that hold in the chicken genome. Significant linear correlations were
found among the regions studied—coding sequences (and their first, second, and third codon positions), flanking regions (5′
and 3′), and introns—as is the case in the human genome. We found that these compositional correlations are not limited to
global GC levels but even extend to individual bases. Furthermore, an analysis of 1037 coding sequences has confirmed a correlation
among GC3, GC2, and GC1. The implications of these results are discussed.
Received: 9 December 1998 / Accepted: 18 April 1999 相似文献
15.
16.
Nicolas Glansdorff 《Journal of molecular evolution》1999,49(4):432-438
We present a hypothesis suggesting that close linkage of functionally related anabolic genes and their ultimate integration
into operons developed under selective pressure as a molecular strategy which contributed to the viability of ancestral thermophilic
cells. Cotranslation of functionally related proteins is viewed as having facilitated the formation of multienzyme complexes
channeling thermolabile substrates and the mutual stabilization of inherently thermolabile proteins. In this perspective,
the evolutionary scheme considered the most probable is the evolution of both Bacteria and Archaea by thermoreduction (Forterre
1995) from a mesophilic, protoeukaryotic last common ancestor (LCA) endowed with appreciable genetic redundancy. 相似文献
17.
Graziano Pesole Luigi R. Ceci Carmela Gissi Cecilia Saccone Carla Quagliariello 《Journal of molecular evolution》1996,43(5):447-452
We have analyzed the nad3-rps12 locus for eight angiosperms in order to compare the utility of mitochondrial DNA and edited mRNA sequences in phylogenetic
reconstruction. The two coding regions, containing from 25 to 35 editing sites in the various plants, have been concatenated
in order to increase the significance of the analysis. Differing from the corresponding chloroplast sequences, unedited mitochondrial
DNA sequences seem to evolve under a quasi-neutral substitution process which undifferentiates the nucleotide substitution
rates for the three codon positions. By using complete gene sequences (all codon positions) we found that genomic sequences
provide a classical angiosperm phylogenetic tree with a clear-cut grouping of monocotyledons and dicotyledons with Magnoliidae
at the basal branch of the tree. Conversely, owing to their low nucleotide substitution rates, edited mRNA sequences were
found not to be suitable for studying phylogenetic relationships among angiosperms.
Received: 24 January 1996 / Accepted: 5 June 1996 相似文献
18.
M.K. Tan 《Journal of molecular evolution》1997,44(6):637-645
Studies of the distribution of the three group I introns (intron A, intron T, and intron AT) in the 26S rDNA of Gaeumannomyces graminis had suggested that they were transferred to a common ancestor of G. graminis var. avenae and var. tritici after it had branched off from var. graminis. Intron AT and intron A exhibited vertical inheritance and coevolved in concert with their hosts. Intron loss could occur
after its acquisition. Loss of any one of the three introns could occur in var. tritici whereas only loss of intron T had been found in the majority of var. avenae isolates. The existence of isolates of var. tritici and var. avenae with three introns suggested that intron loss could be reversed by intron acquisition and that the whole process is a dynamic
one. This process of intron acquisition and intron loss reached different equilibrium points for different varieties and subgroups,
which explained the irregular distribution of these introns in G. graminis. Each of the three group I introns was more closely related to other intron sequences that share the same insertion point
in the 26S rDNA than to each other. These introns in distantly related organisms appeared to have a common ancestry. This
system had provided a good model for studies on both the lateral transfer and common ancestry of group I introns in the 26S
rRNA genes.
Received: 17 May 1996 / Accepted: 14 January 1997 相似文献
19.
Peeters NM Chapron A Giritch A Grandjean O Lancelin D Lhomme T Vivrel A Small I 《Journal of molecular evolution》2000,50(5):413-423
Two cysteinyl-tRNA synthetases (CysRS) and four asparaginyl-tRNA synthetases (AsnRS) from Arabidopsis thaliana were characterized from genome sequence data, EST sequences, and RACE sequences. For one CysRS and one AsnRS, sequence alignments
and prediction programs suggested the presence of an N-terminal organellar targeting peptide. Transient expression of these
putative targeting sequences joined to jellyfish green fluorescent protein (GFP) demonstrated that both presequences can efficiently
dual-target GFP to mitochondria and plastids. The other CysRS and AsnRSs lack targeting sequences and presumably aminoacylate
cytosolic tRNAs. Phylogenetic analysis suggests that the four AsnRSs evolved by repeated duplication of a gene transferred
from an ancestral plastid and that the CysRSs also arose by duplication of a transferred organelle gene (possibly mitochondrial).
These case histories are the best examples to date of capture of organellar aminoacyl-tRNA synthetases by the cytosolic protein
synthesis machinery.
Received: 8 October 1999 / Accepted: 23 January 2000 相似文献
20.
Moulton V Gardner PP Pointon RF Creamer LK Jameson GB Penny D 《Journal of molecular evolution》2000,51(4):416-421
Opinion is strongly divided on whether life arose on earth under hot or cold conditions, the hot-start and cold-start scenarios,
respectively. The origin of life close to deep thermal vents appears as the majority opinion among biologists, but there is
considerable biochemical evidence that high temperatures are incompatible with an RNA world. To be functional, RNA has to
fold into a three-dimensional structure. We report both theoretical and experimental results on RNA folding and show that
(as expected) hot conditions strongly reduce RNA folding. The theoretical results come from energy-minimization calculations
of the average extent of folding of RNA, mainly from 0–90°C, for both random sequences and tRNA sequences. The experimental
results are from circular-dichroism measurements of tRNA over a similar range of temperatures. The quantitative agreement
between calculations and experiment is remarkable, even to the shape of the curves indicating the cooperative nature of RNA
folding and unfolding. These results provide additional evidence for a lower temperature stage being necessary in the origin
of life.
Received: 1 March 2000 / Accepted: 14 June 2000 相似文献