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1.
The Root of the Universal Tree of Life Inferred from Anciently Duplicated Genes Encoding Components of the Protein-Targeting Machinery 总被引:5,自引:0,他引:5
The key protein of the signal recognition particle (termed SRP54 for Eucarya and Ffh for Bacteria) and the protein (termed
SRα for Eucarya and Ftsy for bacteria) involved in the recognition and binding of the ribosome SRP nascent polypeptide complex
are the products of an ancient gene duplication that appears to predate the divergence of all extant taxa. The paralogy of
the genes encoding the two proteins (both of which are GTP triphosphatases) is argued by obvious sequence similarities between
the N-terminal half of SRP54(Ffh) and the C-terminal half of SRα(Ftsy). This enables a universal phylogeny based on either
protein to be rooted using the second protein as an outgroup. Phylogenetic trees inferred by various methods from an alignment
(220 amino acid positions) of the shared SRP54(Ffh) and SRα(Ftsy) regions generate two reciprocally rooted universal trees
corresponding to the two genes. The root of both trees is firmly positioned between Bacteria and Archaea/Eucarya, thus providing
strong support for the notion (Iwabe et al. 1989; Gogarten et al. 1989) that the first bifurcation in the tree of life separated
the lineage leading to Bacteria from a common ancestor to Archaea and Eucarya. None of the gene trees inferred from the two
paralogues support a paraphyletic Archaea with the crenarchaeota as a sister group to Eucarya.
Received: 19 March 1998 / Accepted: 5 June 1998 相似文献
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.
The amino acid sequences of 22 α-amylases from family 13 of glycosyl hydrolases were analyzed with the aim of revealing the
evolutionary relationships between the archaeal α-amylases and their eubacterial and eukaryotic counterparts. Two evolutionary
distance trees were constructed: (i) the first one based on the alignment of extracted best-conserved sequence regions (58
residues) comprising β2, β3, β4, β5, β7, and β8 strand segments of the catalytic (α/β)8-barrel and a short conserved stretch in domain B protruding out of the barrel in the β3 →α3 loop, and (ii) the second one
based on the alignment of the substantial continuous part of the (α/β)8-barrel involving the entire domain B (consensus length: 386 residues). With regard to archaeal α-amylases, both trees compared
brought, in fact, the same results; i.e., all family 13 α-amylases from domain Archaea were clustered with barley pI isozymes,
which represent all plant α-amylases. The enzymes from Bacillus licheniformis and Escherichia coli, representing liquefying and cytoplasmic α-amylases, respectively, seem to be the further closest relatives to archaeal α-amylases.
This evolutionary relatedness clearly reflects the discussed similarities in the amino acid sequences of these α-amylases,
especially in the best-conserved sequence regions. Since the results for α-amylases belonging to all three domains (Eucarya,
Eubacteria, Archaea) offered by both evolutionary trees are very similar, it is proposed that the investigated conserved sequence
regions may indeed constitute the ``sequence fingerprints' of a given α-amylase.
Received: 3 June 1998 / Accepted: 20 August 1998 相似文献
4.
The members of the PKA regulatory subunit family (PKA-R family) were analyzed by multiple sequence alignment and clustering
based on phylogenetic tree construction. According to the phylogenetic trees generated from multiple sequence alignment of
the complete sequences, the PKA-R family was divided into four subfamilies (types I to IV). Members of each subfamily were
exclusively from animals (types I and II), fungi (type III), and alveolates (type IV). Application of the same methodology
to the cAMP-binding domains, and subsequently to the region delimited by β-strands 6 and 7 of the crystal structures of bovine
RIα and rat RIIβ (the phosphate-binding cassette; PBC), proved that this highly conserved region was enough to classify unequivocally
the members of the PKA-R family. A single signature sequence, F–G–E–[LIV]–A–L–[LIMV]–x(3)–[PV]–R–[ANQV]–A, corresponding to
the PBC was identified which is characteristic of the PKA-R family and is sufficient to distinguish it from other members
of the cyclic nucleotide-binding protein superfamily. Specific determinants for the A and B domains of each R-subunit type
were also identified. Conserved residues defining the signature motif are important for interaction with cAMP or for positioning
the residues that directly interact with cAMP. Conversely, residues that define subfamilies or domain types are not conserved
and are mostly located on the loop that connects α-helix B′ and β strand 7.
Received: 2 November 2000/Accepted: 14 June 2001 相似文献
5.
James R. Brown Frank T. Robb Robert Weiss W. Ford Doolittle 《Journal of molecular evolution》1997,45(1):9-16
Each amino acid is attached to its cognate tRNA by a distinct aminoacyl-tRNA synthetase (aaRS). The conventional evolutionary
view is that the modern complement of synthetases existed prior to the divergence of eubacteria and eukaryotes. Thus comparisons
of prokaryotic and eukaryotic aminoacyl-tRNA synthetases of the same type (charging specificity) should show greater sequence
similarities than comparisons between synthetases of different types—and this is almost always so. However, a recent study
[Ribas de Pouplana L, Furgier M, Quinn CL, Schimmel P (1996) Proc Natl Acad Sci USA 93:166–170] suggested that tryptophanyl- (TrpRS) and tyrosyl-tRNA (TyrRS) synthetases of the Eucarya (eukaryotes) are more
similar to each other than either is to counterparts in the Bacteria (eubacteria). Here, we reexamine the evolutionary relationships
of TyrRS and TrpRS using a broader range of taxa, including new sequence data from the Archaea (archaebacteria) as well as
species of Eucarya and Bacteria. Our results differ from those of Ribas de Pouplana et al.: All phylogenetic methods support
the separate monophyly of TrpRS and TyrRS. We attribute this result to the inclusion of the archaeal data which might serve
to reduce long branch effects possibly associated with eukaryotic TrpRS and TyrRS sequences. Furthermore, reciprocally rooted
phylogenies of TrpRS and TyrRS sequences confirm the closer evolutionary relationship of Archaea to eukaryotes by placing
the root of the universal tree in the Bacteria.
Received: 7 December 1996 / Accepted: 11 February 1997 相似文献
6.
A heuristic approach to search for the maximum-likelihood (ML) phylogenetic tree based on a genetic algorithm (GA) has been
developed. It outputs the best tree as well as multiple alternative trees that are not significantly worse than the best one
on the basis of the likelihood criterion. These near-optimum trees are subjected to further statistical tests. This approach
enables ones to infer phylogenetic trees of over 20 taxa taking account of the rate heterogeneity among sites on practical
time scales on a PC cluster. Computer simulations were conducted to compare the efficiency of the present approach with that
of several likelihood-based methods and distance-based methods, using amino acid sequence data of relatively large (5–24)
taxa. The superiority of the ML method over distance-based methods increases as the condition of simulations becomes more
realistic (an incorrect model is assumed or many taxa are involved). This approach was applied to the inference of the universal
tree based on the concatenated amino acid sequences of vertically descendent genes that are shared among all genomes whose
complete sequences have been reported. The inferred tree strongly supports that Archaea is paraphyletic and Eukarya is specifically
related to Crenarchaeota. Apart from the paraphyly of Archaea and some minor disagreements, the universal tree based on these
genes is largely consistent with the universal tree based on SSU rRNA.
Received: 4 January 2001 / Accepted: 16 May 2001 相似文献
7.
Wytze T. Stam Jaap J. Beintema Rossana D’Avino Maurizio Tamburrini Guido di Prisco 《Journal of molecular evolution》1997,45(4):437-445
Amino acid sequences of α- and β-chains of human hemoglobin and of hemoglobins of coelacanth and 24 teleost fish species,
including 11 antarctic and two temperate Notothenioidei, were analyzed using maximum parsimony. Trees were derived for the
α- and β-chains separately and for tandemly arranged sequences, using the human and coelacanth sequences as outgroups in all
analyses. The topologies of the trees of the α-and β-chains are highly congruent and indicate a specific pattern of gene duplications
and gene expression of teleost hemoglobins which has not yet been investigated into more detail. The Notothenioid fish generally
contain a single major hemoglobin and often a second minor component. The α- and β-chains of the major components form a monophyletic
group in all investigated trees, with the nonantarctic Pseudaphritis as their sister taxon. The minor chains also are a monophyletic group and form an unresolved cluster with the major chains
and the hemoglobins of tuna and red gurnard. The Notothenioid families Nototheniidae and Bathydraconidae appear to be paraphyletic.
Received: 26 March 1997 / Accepted: 7 May 1997 相似文献
8.
Hiroshi Wada Mari Kobayashi Riki Sato Nori Satoh Hitoshi Miyasaka Yoshihisa Shirayama 《Journal of molecular evolution》2002,54(1):118-128
To test the validity of intron–exon structure as a phylogenetic marker, the intron–exon structure of EF-1α genes was investigated
for starfish, acornworms, ascidians, larvaceans, and amphioxus and compared with that of vertebrates. Of the 11 distinct intron
insertion sites found within the coding regions of the deuterostome EF-1α genes, 7 are shared by several taxa, while the remainder
are unique to certain taxa. Examination of the shared introns of the deuterostome EF-1α gene revealed that independent intron
loss or intron insertion must have occurred in separate lineages of the deuterostome taxa. Maximum parsimony analysis of the
intron–exon data matrix recovered five parsimonious trees (consistency index = 0.867). From this result, we concluded that
the intron–exon structure of deuterostome EF-1α has evolved more dynamically than previously thought, rendering it unsuitable
as a phylogenetic marker. We also reconstructed an evolutionary history of intron insertion–deletion events on the deuterostome
phylogeny, based on several molecular phylogenetic studies. These analyses revealed that the deuterostome EF-1α gene has lost
individual introns more frequently than all introns simultaneously. 相似文献
9.
Bocchetta M Gribaldo S Sanangelantoni A Cammarano P 《Journal of molecular evolution》2000,50(4):366-380
The phylogenetic placement of the Aquifex and Thermotoga lineages has been inferred from (i) the concatenated ribosomal proteins S10, L3, L4, L23, L2, S19, L22, and S3 encoded in
the S10 operon (833 aa positions); (ii) the joint sequences of the elongation factors Tu(1α) and G(2) coded by the str operon tuf and fus genes (733 aa positions); and (iii) the joint RNA polymerase β- and β′-type subunits encoded in the rpoBC operon (1130 aa positions). Phylogenies of r-protein and EF sequences support with moderate (r-proteins) to high statistical confidence (EFs) the placement of the two hyperthermophiles at the base of the bacterial clade
in agreement with phylogenies of rRNA sequences. In the more robust EF-based phylogenies, the branching of Aquifex and Thermotoga below the successive bacterial lineages is given at bootstrap proportions of 82% (maximum likelihood; ML) and 85% (maximum
parsimony; MP), in contrast to the trees inferred from the separate EF-Tu(1α) and EF-G(2) data sets, which lack both resolution
and statistical robustness. In the EF analysis MP outperforms ML in discriminating (at the 0.05 level) trees having A. pyrophilus and T. maritima as the most basal lineages from competing alternatives that have (i) mesophiles, or the Thermus genus, as the deepest bacterial radiation and (ii) a monophyletic A. pyrophilus–T. maritima cluster situated at the base of the bacterial clade. RNAP-based phylogenies are equivocal with respect to the Aquifex and Thermotoga placements. The two hyperthermophiles fall basal to all other bacterial phyla when potential artifacts contributed by the
compositionally biased and fast-evolving Mycoplasma genitalium and Mycoplasma pneumoniae sequences are eschewed. However, the branching order of the phyla is tenuously supported in ML trees inferred by the exhaustive
search method and is unresolved in ML trees inferred by the quartet puzzling algorithm. A rooting of the RNA polymerase-subunit
tree at the mycoplasma level seen in both the MP trees and the ML trees reconstructed with suboptimal amino acid substitution
models is not supported by the EF-based phylogenies which robustly affiliate mycoplasmas with low-G+C gram-positives and,
most probably, reflects a ``long branch attraction' artifact.
Received: 22 September 1999 / Accepted: 11 January 2000 相似文献
10.
Bernard Labedan Anne Boyen Margot Baetens Daniel Charlier Pingguo Chen Raymond Cunin Virginie Durbeco Nicolas Glansdorff Guy Herve Christianne Legrain Ziyuan Liang Christina Purcarea Martine Roovers Rony Sanchez Thia-Lin Toong Marc Van de Casteele Françoise van Vliet Ying Xu Yuan-Fu Zhang 《Journal of molecular evolution》1999,49(4):461-473
Forty-four sequences of ornithine carbamoyltransferases (OTCases) and 33 sequences of aspartate carbamoyltransferases (ATCases)
representing the three domains of life were multiply aligned and a phylogenetic tree was inferred from this multiple alignment.
The global topology of the composite rooted tree (each enzyme family being used as an outgroup to root the other one) suggests
that present-day genes are derived from paralogous ancestral genes which were already of the same size and argues against
a mechanism of fusion of independent modules. A closer observation of the detailed topology shows that this tree could not
be used to assess the actual order of organismal descent. Indeed, this tree displays a complex topology for many prokaryotic
sequences, with polyphyly for Bacteria in both enzyme trees and for the Archaea in the OTCase tree. Moreover, representatives
of the two prokaryotic Domains are found to be interspersed in various combinations in both enzyme trees. This complexity
may be explained by assuming the occurrence of two subfamilies in the OTCase tree (OTC α and OTC β) and two other ones in
the ATCase tree (ATC I and ATC II). These subfamilies could have arisen from duplication and selective losses of some differentiated
copies during the successive speciations. We suggest that Archaea and Eukaryotes share a common ancestor in which the ancestral
copies giving the present-day ATC II/OTC β combinations were present, whereas Bacteria comprise two classes: one containing
the ATC II/OTC α combination and the other harboring the ATC I/OTC β combination. Moreover, multiple horizontal gene transfers
could have occurred rather recently amongst prokaryotes. Whichever the actual history of carbamoyltransferases, our data suggest
that the last common ancestor to all extant life possessed differentiated copies of genes coding for both carbamoyltransferases,
indicating it as a rather sophisticated organism. 相似文献
11.
Julius Lukeš Milan Jirků David Doležel Ivica Kral'ová Laura Hollar Dmitri A. Maslov 《Journal of molecular evolution》1997,44(5):521-527
To further investigate the phylogeny of protozoa from the order Kinetoplastida we have sequenced the small subunit (SSU)
and a portion of the large subunit (LSU) nuclear rRNA genes. The SSU and LSU sequences were determined from a lizard trypanosome,
Trypanosoma scelopori and a bodonid, Rhynchobodo sp., and the LSU sequences were determined from an insect trypanosomatid, Crithidia oncopelti, and a bodonid, Dimastigella trypaniformis. Contrary to previous results, in which trypanosomes were found to be paraphyletic, with Trypanosoma brucei representing the earliest-diverging lineage, we have now found evidence for the monophyly of trypanosomes. Addition of new
taxa which subdivide long branches (such as that of T. brucei) have helped to identify homoplasies responsible for the paraphyletic trees in previous studies. Although the monophyly of
the trypanosome clade is supported in the bootstrap analyses for maximum likelihood at 97% and maximum parsimony at 92%, there
is only a small difference in ln-likelihood value or tree length between the most optimal monophyletic tree and the best suboptimal
paraphyletic tree. Within the trypanosomatid subtree, the clade of trypanosomes is a sister group to the monophyletic clade
of the nontrypanosome genera. Different groups of trypanosomes group on the tree according to their mode of transmission.
This suggests that the adaptation to invertebrate vectors plays a more important role in the trypanosome evolution than the
adaptation to vertebrate hosts.
Received: 5 July 1996 / Accepted: 26 September 1996 相似文献
12.
Ayako Yamamoto Tetsuo Hashimoto Emiko Asaga Masami Hasegawa Nobuichi Goto 《Journal of molecular evolution》1997,44(1):98-105
Major parts of amino-acid-coding regions of elongation factor (EF)-1α and EF-2 in Trichomonas tenax were amplified by PCR from total genomic DNA and the products were cloned into a plasmid vector, pGEM-T. The three clones
from each of the products of the EF-1α and EF-2 were isolated and sequenced. The insert DNAs of the clones containing EF-1α
coding regions were each 1,185 bp long with the same nucleotide sequence and contained 53.1% of G + C nucleotides. Those of
the clones containing EF-2 coding regions had two different sequences; one was 2,283 bp long and the other was 2,286 bp long,
and their G + C contents were 52.5 and 52.9%, respectively. The copy numbers of the EF-1α and EF-2 gene per chromosome were
estimated as four and two, respectively.
The deduced amino acid sequences obtained by the conceptual translation were 395 residues from EF-1α and 761 and 762 residues
from the EF-2s. The sequences were aligned with the other eukaryotic and archaebacterial EF-1αs and EF-2s, respectively.
The phylogenetic position of T. tenax was inferred by the maximum likelihood (ML) method using the EF-1α and EF-2 data sets. The EF-1α analysis suggested that
three mitochondrion-lacking protozoa, Glugea plecoglossi, Giardia lamblia, and T. tenax, respectively, diverge in this order in the very early phase of eukaryotic evolution. The EF-2 analysis also supported the
divergence of T. tenax to be immediately next to G. lamblia.
Received: 15 February 1996 / Accepted: 28 June 1996 相似文献
13.
Suga H Koyanagi M Hoshiyama D Ono K Iwabe N Kuma K Miyata T 《Journal of molecular evolution》1999,48(6):646-653
To know whether genes involved in cell–cell communication typical of multicellular animals dramatically increased in concert
with the Cambrian explosion, the rapid evolutionary burst in the major groups of animals, and whether these genes exist in
the sponge lacking cell cohesiveness and coordination typical of eumetazoans, we have carried out cloning of the G-protein
α subunit (Gα) and the protein tyrosine kinase (PTK) cDNAs from Ephydatia fluviatilis (freshwater sponge) and Hydra magnipapillata strain 105 (hydra). We obtained 13 Gα and 20 PTK cDNAs. Generally animal gene families diverged first by gene duplication
(subtype duplication) that gave rise to diverse subtypes with different primary functions, followed by further gene duplication
in the same subtype (isoform duplication) that gave rise to isoform genes with virtually identical function. Phylogenetic
trees of Gα and PTK families including cDNAs from sponge and hydra revealed that most of the present-day subtypes had been
established in the very early evolution of animals before the parazoan–eumetazoan split, the earliest branching among the
extant animal phyla, by extensive subtype duplication: for PTK and Gα families, 23 and 9 subtype duplications were observed
in the early stage before the parazoan–eumetazoan split, respectively, and after that split, only 2 and 1 subtype duplications
were found, respectively. After the separation from arthropods, vertebrates underwent frequent isoform duplications before
the fish–tetrapod split. Furthermore, rapid amino acid changes appear to have occurred in concert with the extensive subtype
duplication and isoform duplication. Thus the pattern of gene diversification during animal evolution might be characterized
by bursts of gene duplication interrupted by considerably long periods of silence, instead of proceeding gradually, and there
might be no direct link between the Cambrian explosion and the extensive gene duplication that generated diverse functions
(subtypes) of these families.
Received: 4 November 1998 / Accepted: 17 November 1998 相似文献
14.
The ribosomal protection proteins (RPPs) mediate the resistance to tetracycline (TC) in Gram-positive and Gram-negative bacteria.
The RPPs display sequence similarity to translation elongation factors, EF-G/EF-2 and EF-Tu/EF-1α. To determine the evolutionary
origin of the RPPs, we constructed a composite phylogenetic tree of the RPPs, EF-G/EF-2 and EF-Tu/EF-1α. This tree includes
two universal trees for the EF-G/EF-2 and EF-Tu/EF-1α, which form clusters corresponding to the respective two groups of proteins
from three superkingdoms. The cluster of RPPs was placed at a point between the EF-G/EF-2 and EF-Tu/EF-1α clusters. The branch
length (substitutions/site) between the node for the RPP cluster and the primary divergence of the RPPs was statistically
shorter than that between the node for this cluster and the primary divergence in the EF-G/EF-2 cluster. This indicates that
the RPPs derived through duplication and divergence of the ancient GTPase before the divergence of the three superkingdoms.
Furthermore, this suggests the RPPs’ extant function occurred before the streptomycetes that include the TC-producing strains.
Therefore, the RPPs evolved independent of the presence of TCs and serve a function other than antibiotic resistance. The
RPPs may provide ribosomal protection against other chemical substances in the environment.
Reviewing
Editor: Dr. Margaret Riley
Takeshi Kobayashi, Lisa Nonaka have contributed significantly to the research and preparation of this article. 相似文献
15.
Mitochondrial Genes Collectively Suggest the Paraphyly of Crustacea with Respect to Insecta 总被引:9,自引:0,他引:9
Erik García-Machado Malgorzata Pempera Nicole Dennebouy Mario Oliva-Suarez Jean-Claude Mounolou Monique Monnerot 《Journal of molecular evolution》1999,49(1):142-149
Complete sequences of seven protein coding genes from Penaeus notialis mitochondrial DNA were compared in base composition and codon usage with homologous genes from Artemia franciscana and four insects. The crustacean genes are significantly less A + T-rich than their counterpart in insects and the pattern
of codon usage (ratio of G + C-rich versus A + T-rich codon) is less biased. A phylogenetic analysis using amino acid sequences
of the seven corresponding polypeptides supports a sister-taxon status for mollusks–annelid and arthropods. Furthermore, a
distance matrix-based tree and two most-parsimonious trees both suggest that crustaceans are paraphyletic with respect to
insects. This is also supported by the inclusion of Panulirus argus COII (complete) and COI and COIII (partial) sequence data. From analysis of single and combined genes to infer phylogenies,
it is observed that obtained from single genes are not well supported in most topologies cases and notably differ from that
of the tree based on all seven genes.
Received: 25 August 1998 / Accepted: 8 March 1999 相似文献
16.
The Origin of Chlorarachniophyte Plastids, as Inferred from Phylogenetic Comparisons of Amino Acid Sequences of EF-Tu 总被引:4,自引:0,他引:4
Ken-ichiro Ishida Ying Cao Masami Hasegawa Norihiro Okada Yoshiaki Hara 《Journal of molecular evolution》1997,45(6):682-687
A molecular phylogenetic analysis of elongation factor Tu (EF-Tu) proteins from plastids was performed in an attempt to identify
the origin of chlorarachniophyte plastids, which are considered to have evolved from the endosymbiont of a photosynthetic
eukaryote. Partial sequences of the genes for plastid EF-Tu proteins (1,080–1,089 bp) were determined for three algae that
contain chlorophyll b, namely, Gymnochlora stellata (Chlorarachniophyceae), Bryopsis maxima (Ulvophyceae), and Pyramimonas disomata (Prasinophyceae). The deduced amino acid sequences were used to construct phylogenetic trees of the plastid and bacterial
EF-Tu proteins by the maximum likelihood, the maximum parsimony, and the neighbor joining methods.
The trees obtained in the present analysis suggest that all plastids that contain chlorophyll b are monophyletic and that the chlorarachniophyte plastids are closely related to those of the Ulvophyceae. The phylogenetic
trees also suggest that euglenophyte plastids are closely related to prasinophycean plastids. The results indicate that the
chlorarachniophyte plastids evolved from a green algal endosymbiont that was closely related to the Ulvophyceae and that at
least two secondary endosymbiotic events have occurred in the lineage of algae with plastids that contain chlorophyll b.
Received: 10 March 1997 / Accepted: 28 July 1997 相似文献
17.
Carolyn J. Lawrence Russell L. Malmberg Michael G. Muszynski R. Kelly Dawe 《Journal of molecular evolution》2002,54(1):42-53
We have reconstructed the evolution of the anciently derived kinesin superfamily using various alignment and tree-building
methods. In addition to classifying previously described kinesins from protists, fungi, and animals, we analyzed a variety
of kinesin sequences from the plant kingdom including 12 from Zea mays and 29 from Arabidopsis thaliana. Also included in our data set were four sequences from the anciently diverged amitochondriate protist Giardia lamblia. The overall topology of the best tree we found is more likely than previously reported topologies and allows us to make the
following new observations: (1) kinesins involved in chromosome movement including MCAK, chromokinesin, and CENP-E may be
descended from a single ancestor; (2) kinesins that form complex oligomers are limited to a monophyletic group of families;
(3) kinesins that crosslink antiparallel microtubules at the spindle midzone including BIMC, MKLP, and CENP-E are closely
related; (4) Drosophila NOD and human KID group with other characterized chromokinesins; and (5) Saccharomyces SMY1 groups with kinesin-I sequences, forming a family of kinesins capable of class V myosin interactions. In addition, we
found that one monophyletic clade composed exclusively of sequences with a C-terminal motor domain contains all known minus
end-directed kinesins.
Received: 20 February 2001 / Accepted: 5 June 2001 相似文献
18.
The aldo-keto reductase enzymes comprise a functionally diverse gene family which catalyze the NADPH-dependant reduction
of a variety of carbonyl compounds. The protein sequences of 45 members of this family were aligned and phylogenetic trees
were deduced from this alignment using the neighbor-joining and Fitch algorithms. The branching order of these trees indicates
that the vertebrate enzymes cluster in three groups, which have a monophyletic origin distinct from the bacterial, plant,
and invertebrate enzymes. A high level of conservation was observed between the vertebrate hydroxysteroid dehydrogenase enzymes,
prostaglandin F synthase, and ρ-crystallin of Xenopus laevis. We infer from the phylogenetic analysis that prostaglandin F synthase may represent a recent recruit to the eicosanoid biosynthetic
pathway from the hydroxysteroid dehydrogenase pathway and furthermore that, in the context of gene recruitment, Xenopus laevisρ-crystallin may represent a shared gene.
Received: 26 August 1996 / Accepted: 5 June 1997 相似文献
19.
Heat Shock Protein 70 Family: Multiple Sequence Comparisons, Function, and Evolution 总被引:14,自引:0,他引:14
The heat shock protein 70 kDa sequences (HSP70) are of great importance as molecular chaperones in protein folding and transport.
They are abundant under conditions of cellular stress. They are highly conserved in all domains of life: Archaea, eubacteria,
eukaryotes, and organelles (mitochondria, chloroplasts). A multiple alignment of a large collection of these sequences was
obtained employing our symmetric-iterative ITERALIGN program (Brocchieri and Karlin 1998). Assessments of conservation are
interpreted in evolutionary terms and with respect to functional implications. Many archaeal sequences (methanogens and halophiles)
tend to align best with the Gram-positive sequences. These two groups also miss a signature segment [about 25 amino acids
(aa) long] present in all other HSP70 species (Gupta and Golding 1993). We observed a second signature sequence of about 4
aa absent from all eukaryotic homologues, significantly aligned in all prokaryotic sequences. Consensus sequences were developed
for eight groups [Archaea, Gram-positive, proteobacterial Gram-negative, singular bacteria, mitochondria, plastids, eukaryotic
endoplasmic reticulum (ER) isoforms, eukaryotic cytoplasmic isoforms]. All group consensus comparisons tend to summarize better
the alignments than do the individual sequence comparisons. The global individual consensus ``matches' 87% with the consensus
of consensuses sequence. A functional analysis of the global consensus identifies a (new) highly significant mixed charge
cluster proximal to the carboxyl terminus of the sequence highlighting the hypercharge run EEDKKRRER (one-letter aa code used).
The individual Archaea and Gram-positive sequences contain a corresponding significant mixed charge cluster in the location
of the charge cluster of the consensus sequence. In contrast, the four Gram-negative proteobacterial sequences of the alignment
do not have a charge cluster (even at the 5% significance level). All eukaryotic HSP70 sequences have the analogous charge
cluster. Strikingly, several of the eukaryotic isoforms show multiple mixed charged clusters. These clusters were interpreted
with supporting data related to HSP70 activity in facilitating chaperone, transport, and secretion function. We observed that
the consensus contains only a single tryptophan residue and a single conserved cysteine. This is interpreted with respect
to the target rule for disaggregating misfolded proteins. The mitochondrial HSP70 connections to bacterial HSP70 are analyzed,
suggesting a polyphyletic split of Trypanosoma and Leishmania protist mitochondrial (Mt) homologues separated from Mt-animal/fungal/plant homologues. Moreover, the HSP70 sequences from
the amitochondrial Entamoeba histolytica and Trichomonas vaginalis species were analyzed. The E. histolytica HSP70 is most similar to the higher eukaryotic cytoplasmic sequences, with significantly weaker alignments to ER sequences
and much diminished matching to all eubacterial, mitochondrial, and chloroplast sequences. This appears to be at variance
with the hypothesis that E. histolytica rather recently lost its mitochondrial organelle. T. vaginalis contains two HSP70 sequences, one Mt-like and the second similar to eukaryotic cytoplasmic sequences suggesting two diverse
origins.
Received: 29 January 1998 / Accepted: 14 May 1998 相似文献
20.
The phylogenetic position of hagfishes in vertebrate evolution is currently controversial. The 18S and 28S rRNA trees support
the monophyly of hagfishes and lampreys. In contrast, the mitochondrial DNAs suggest the close association of lampreys and
gnathostomes. To clarify this controversial issue, we have conducted cloning and sequencing of the four nuclear DNA–coded
single-copy genes encoding the triose phosphate isomerase, calreticulin, and the largest subunit of RNA polymerase II and
III. Based on these proteins, together with the Mn superoxide dismutase for which hagfish and lamprey sequences are available
in database, phylogenetic trees have been inferred by the maximum likelihood (ML) method of protein phylogeny. It was shown
that all the five proteins prefer the monophyletic tree of cyclostomes, and the total log-likelihood of the five proteins
significantly supports the cyclostome monophyly at the level of ±1 SE. The ML trees of aldolase family comprising three nonallelic
isoforms and the complement component group comprising C3, C4, and C5, both of which diverged during vertebrate evolution
by gene duplications, also suggest the cyclostome monophyly.
Received: 28 April 1999 / Accepted: 30 June 1999 相似文献