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1.
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
2.
Of Worms and Men: An Evolutionary Perspective on the Fibroblast Growth Factor (FGF) and FGF Receptor Families 总被引:6,自引:0,他引:6
François Coulier Pierre Pontarotti Régine Roubin Helge Hartung Mitchell Goldfarb Daniel Birnbaum 《Journal of molecular evolution》1997,44(1):43-56
FGFs (fibroblast growth factors) play major roles in a number of developmental processes. Recent studies of several human
disorders, and concurrent analysis of gene knock-out and properties of the corresponding recombinant proteins have shown that
FGFs and their receptors are prominently involved in the development of the skeletal system in mammals. We have compared the
sequences of the nine known mammalian FGFs, FGFs from other vertebrates, and three additional sequences that we extracted
from existing databases: two human FGF sequences that we tentatively designated FGF10 and FGF11, and an FGF sequence from
C?norhabditis elegans. Similarly, we have compared the sequences of the four FGF receptor paralogs found in chordates with four non-chordate FGF
receptors, including one recently identified in C. elegans. The comparison of FGF and FGF receptor sequences in vertebrates and nonvertebrates shows that the FGF and FGF receptor families
have evolved through phases of gene duplications, one of which may have coincided with the emergence of vertebrates, in relation
with their new system of body scaffold.
Received: 6 April 1996 / Accepted: 5 July 1996 相似文献
3.
Thirty complete coding sequences of human major histocompatibility complex (Mhc) class II DRB alleles, spanning 237 codons, were analyzed for phylogenetic information using distance, parsimony, and likelihood approaches.
Allelic genealogies derived from different parts of the coding sequence (exon 2, the 5′ and 3′ ends of exon 2, respectively,
and exons 3–6) were compared. Contrary to prior assertions, a rigorous analysis of allelic genealogies in this gene family
cannot be used to justify the claim that the lineage leading to modern humans contained on average at least 100,000 individuals.
Phylogenetic inferences based upon the exon 2 region of the DRB loci are complicated by selection and recombination, so this part of the gene does not provide a complete and accurate view
of allelic relationships. Attempts to reconstruct human history from genetic data must use realistic models which consider
the complicating factors of nonequilibrium populations, recombination, and different patterns of selection.
Received: 19 February 1997 / Accepted: 12 June 1997 相似文献
4.
François Agnès Marguerite-Marie Toux Catherine André Francis Galibert 《Journal of molecular evolution》1997,45(1):43-49
Receptor tyrosine kinases with five, seven, and three Ig-like domains in their extracellular region are grouped in subclasses
IIIa, IIIb, and IIIc, respectively. Here, we describe the genomic organization of the extracellular coding region of the human FGFR4 (IIIc) and FLT4 (IIIb) genes and compare it to that of the human FGFR1(IIIc), KIT, and FMS (IIIa). The results show that while genes belonging to the same subclass have an identical exon/intron structure in their extracellular
coding region—as they do in their intracellular coding region—genes of related subclasses only have a similar exon/intron
structure. These results strongly support the hypothesis that the genes of the three subclasses evolved from a common ancestor
by duplications involving entire genes, already in pieces. Hypotheses on the origin of introns and on the difference in the
number of extracellular Ig-like domains in the three gene subclasses are discussed.
Received: 19 August 1996 / Accepted: 2 January 1997 相似文献
5.
While globin genes ctt-2β and ctt-9.1 in Chironomus thummi thummi each have a single intron, all of the other insect globin genes reported so far are intronless. We analyzed four globin genes
linked to the two intron-bearing genes in C. th. thummi. Three have a single intron at the same position as ctt-2β and ctt-9.1; the fourth is intronless and lies between intron bearing genes. Finally, in addition to its intron, one gene (ctt-13RT) was recently interrupted by retrotransposition. Phylogenetic analyses show that the six genes in C. th. thummi share common ancestry with five globin genes in the distantly related species C. tentans, and that a 5-gene ancestral cluster predates the divergence of the two species. One gene in the ancestral cluster gave rise
to ctn-ORFB in C. tentans, and duplicated in C. th. thummi to create ctt-11 and ctt-12. From parsimonious calculations of evolutionary distances since speciation, ctt-11, ctt-12, and ctn-ORFB evolved rapidly, while ctn-ORFE in C. tentans evolved slowly compared to other globin genes in the clusters. While these four globins are under selective pressure, we
suggest that most chironomid globin genes were not selected for their unique function. Instead, we propose that high gene
copy number itself was selected because conditions favored organisms that could synthesize more hemoglobin. High gene copy
number selection to produce more of a useful product may be the basis of forming multigene families, all of whose members
initially accumulate neutral substitutions while retaining essential function. Maintenance of a large family of globin genes
not only ensured high levels of hemoglobin production, but may have facilitated the extensive divergence of chironomids into
as many as 5000 species.
Received: 31 December 1996 / Accepted: 16 May 1997 相似文献
6.
Yi-Hong Zhou David Hewett-Emmett Jeannette P. Ward Wen-Hsiung Li 《Journal of molecular evolution》1997,45(6):610-618
Bush babies have had a long history of nocturnal life and it would be interesting to know whether their color vision genes
have become degenerate. Therefore, we used PCR techniques to sequence the X-linked pigment gene of two of these nocturnal
prosimians: Galago senegalensis and Otolemur garnettii. Southern hybridization of genomic DNA of G. senegalensis showed a single X-linked pigment gene. Interestingly, the deduced pigment sequences of the two bush babies are identical.
By comparing the X-linked pigments of bush baby, human, squirrel monkey, and marmoset, 38 variable positions were identified.
At those positions that may cause a spectral shift, the bush baby pigment has identical or biochemically similar residues
to those of the marmoset cone pigment with a spectral peak of 543 nm. This result is consistent with the estimate of 544–545
nm for the spectral peak of the X-linked pigment of Otolemur crassicaudatus, which is closely related to Otolemur garnettii. The neighbor-joining tree of mammalian X-linked pigments showed a significantly shorter branch in the bush baby lineage than
in other primate lineages. A relative rate test showed that the nonsynonymous substitution rate of the bush baby X-linked
pigment gene is about three times slower than that of the human red pigment gene, though the synonymous substitution rates
of the two genes are similar. The slower nonsynonymous rate in the bush baby lineage suggests that the bush baby X-linked
pigment gene is under functional constraints, in spite of its nocturnal life. Two radical changes at positions in the intradiskal
surface next to the sixth transmembrane domain were observed in the X-linked cone pigment of bush babies but not in other
primates. They are changes from Ala to Ser and from Asn to His, which are similar in function to the corresponding residues
in rhodopsins. These two changes may be of importance for dim light sensitivity, which is consistent with our proposal that
the evolution of the bush baby X-linked pigment gene is under selective pressure. In addition, the 2.5% divergence in introns
2 and 5 of the X-linked pigment gene between the two bush babies supports their classification into two separate genera.
Received: 30 November 1996 / Accepted: 17 June 1997 相似文献
7.
The sequences of the entire blue opsin gene in the squirrel monkey (Saimiri boliviensis) and the five introns of the human blue opsin gene were obtained. Intron 3 of these genes contains an Alu sequence and intron
4 contains a partial mer13 sequence. A comparison of the squirrel monkey opsin sequence with published mammalian opsin sequences
shows that features believed to be functionally critical are all conserved. However, the blue opsin has evolved twice as fast
as rhodopsin and is only as conservative as the β globin, which has evolved at the average rate of mammalian proteins. Interestingly,
the interhelical loops are, on average, actually more conservative than the transmembrane α helical regions. The introns of
the blue opsin gene have evolved at the average rate of introns in primate genes.
Received: 5 August 1996 / Accepted: 2 October 1996 相似文献
8.
Jennifer Pastorini Michael R.J. Forstner Robert D. Martin Don J. Melnick 《Journal of molecular evolution》1998,47(1):32-41
The New World monkeys are divided into two main groups, Callitrichidae and Cebidae. Callimico goeldii shares traits with both the Cebidae and the Callitrichidae. Recent morphological phyletic studies generally place Callimico as the most basal member of the Callitrichidae. In contrast, genetic studies (immunological, restriction fragment, and sequence
data) have consistently placed Callimico somewhere within the Callitrichidae, not basal to this clade. A DNA sequence data set from the terminal 236 codons of the
mitochondrial ND4 gene and the tRNAHis, tRNASer, and tRNALeu genes was generated to clarify the position of Callimico. The sequences of 887 base pairs were analyzed by maximum-parsimony, neighbor-joining, and maximum-likelihood methods. The
results of these various methods are generally congruent and place Callimico within the Callitrichidae between the marmosets (Callithrix and Cebuella) and the tamarins (Saguinus and Leontopithecus). Combined analyses of all suitable nuclear and mitochondrial gene sequences confirm the position of Callimico between the marmosets and the tamarins. As available molecular evidence indicates that Callimico is more closely related to the marmosets than to the tamarins, a reconsideration of the morphological evidence in light of
the consensus tree from DNA sequence analyses is warranted. The marmosets and tamarins share four morphological characters
(loss of the third molar, loss of the hypocone, reduced body size, reproductive twinning). Dwarfism may have evolved repeatedly
among the Callitrichidae. It is well-known that the loss of a character can occur many times independently. The reproduction
of marmosets and tamarins is extremely specialized and it is difficult to imagine that this complex and unique twinning system
evolved separately in marmosets and tamarins. However, it is possible that a secondary reversal to single offspring took place
in Callimico.
Received: 20 March 1997 / Accepted: 17 December 1997 相似文献
9.
Ana I. Antón Antonio J. Martínez-Murcia Francisco Rodríguez-Valera 《Journal of molecular evolution》1998,47(1):62-72
The ribosomal RNA multigene family in Escherichia coli comprises seven rrn operons of similar, but not identical, sequence. Four operons (rrnC, B, G, and E) contain genes in the 16S–23S intergenic spacer region (ISR) for tRNAGlu-2 and three (rrnA, D, and H) contain genes for tRNAIle-1 and tRNAAla-1B. To increase our understanding of their molecular evolution, we have determined the ISR sequence of the seven operons in
a set of 12 strains from the ECOR collection. Each operon was specifically amplified using polymerase chain reaction primers
designed from genes or open reading frames located upstream of the 16S rRNA genes in E. coli K12. With a single exception (ECOR 40), ISRs containing one or two tRNA genes were found at the same respective loci as those
of strain K12. Intercistronic heterogeneity already found in K12 was representative of most variation among the strains studied
and the location of polymorphic sites was the same. Dispersed nucleotide substitutions were very few but 21 variable sites
were found grouped in a stem-loop, although the secondary structure was conserved. Some regions were found in which a stretch
of nucleotides was substituted in block by one alternative, apparently unrelated, sequence (as illustrated by the known putative
insertion of rsl in K12). Except for substitutions of different sizes and insertions/deletions found in the ISR, the pattern of nucleotide
variation is very similar to that found for the 16S rRNA gene in E. coli. Strains K12 and ECOR 40 showed the highest intercistronic heterogeneity. Most strains showed a strong tendency to homogenization.
Concerted evolution could explain the notorious conservation of this region that is supposed to have low functional restrictions.
Received: 31 July 1997 / Accepted: 17 October 1997 相似文献
10.
The Peperomia polybotrya coxI gene intron is the only currently reported group I intron in a vascular plant mitochondrial genome and it likely originated
by horizontal transfer from a fungal donor. We provide a clearer picture of the horizontal transfer and a portrayal of the
evolution of the group I intron since it was gained by the Peperomia mitochondrial genome. The intron was transferred recently in terms of plant evolution, being restricted to the single genus
Peperomia among the order Piperales. Additional support is presented for the suggestion that a recombination/repair mechanism was used
by the intron for integration into the Peperomia mitochondrial genome, as a perfect 1:1 correspondence exists between the intron's presence in a species and the presence
of divergent nucleotide markers flanking the intron insertion site. Sequencing of coxI introns from additional Peperomia species revealed that several mutations have occurred in the intron since the horizontal transfer, but sequence alterations
have not caused frameshifts or created stop codons in the intronic open reading frame. In addition, two coxI pseudogenes in Peperomia cubensis were discovered that lack a large region of coxI exon 2 and contain a truncated version of the group I intron that likely cannot be spliced out.
Received: 29 May 1997 / Accepted: 1 November 1997 相似文献
11.
Emmanuel Mertens Uri S. Ladror Jennifer A. Lee Anya Miretsky Andrea Morris Catherine Rozario Robert G. Kemp Miklós Müller 《Journal of molecular evolution》1998,47(6):739-750
The pyrophosphate-dependent phosphofructokinase (PPi-PFK) of the amitochondriate protist Trichomonas vaginalis has been purified. The enzyme is a homotetramer of about 50 kDa subunits and is not subject to allosteric regulation. The
protein was fragmented and a number of peptides were sequenced. Based on this information a PCR product was obtained from
T. vaginalis gDNA and used to isolate corresponding cDNA and gDNA clones. Southern analysis indicated the presence of five genes. One
open reading frame (ORF) was completely sequenced and for two others the 5′ half of the gene was determined. The sequences
were highly similar. The complete ORF corresponded to a polypeptide of about 46 kDa. All the peptide sequences obtained were
present in the derived sequences. The complete ORF was highly similar to that of other PFKs, primarily in its amino-terminal
half. The T. vaginalis enzyme was most similar to PPi-PFK of the mitochondriate heterolobosean, Naegleria fowleri. Most of the residues shown or assumed to be involved in substrate binding in other PPi-PFKs were conserved in the T. vaginalis enzyme. Direct comparison and phylogenetic reconstruction revealed a significant divergence among PPi-PFKs and related enzymes, which can be assigned to at least four distantly related groups, three of which contain enzymes
of protists. The separation of these groups is supported with a high percentage of bootstrap proportions. The short T. vaginalis PFK shares a most recent common ancestor with the enzyme from N. fowleri. This pair is clearly separated from a group comprising the long (>60-kDa) enzymes from Giardia lamblia, Entamoeba histolytica pfk2, the spirochaetes Borrelia burgdorferi and Trepomena pallidum, as well as the α- and β-subunits of plant PPi-PFKs. The third group (``X') containing protist sequences includes the glycosomal ATP-PFK of Trypanosoma brucei, E. histolytica pfk1, and a second sequence from B. burgdorferi. The fourth group (``Y') comprises cyanobacterial and high-G + C, Gram-positive eubacterial sequences. The well-studied PPi-PFK of Propionibacterium freudenreichii is highly divergent and cannot be assigned to any of these groups. These four groups are well separated from typical ATP-PFKs,
the phylogenetic analysis of which confirmed relationships established earlier. These findings indicate a complex history
of a key step of glycolysis in protists with several early gene duplications and possible horizontal gene transfers.
Received: 5 December 1997 / Accepted: 18 March 1998 相似文献
12.
de Kloet SR 《Journal of molecular evolution》2001,53(2):135-143
This study describes the results of an analysis using Southern blotting, the polymerase chain reaction, and sequencing which
shows that the African grey parrot (Psittacus erithacus) lacks the W-chromosomal gene for the alpha subunit of mitochondrial ATP synthase (ATP5A1W). Additional evidence shows that
in other psittacines a fragment of the ATP5A1W gene contains five times as many nonsynonymous nucleotide replacements as the
homologous fragment of the Z gene. Therefore, whereas in these other psittacines the corresponding ATP5A1Z protein fragment
is highly conserved and varies by only a few, moderately conservative amino acid substitutions, the homologous ATP5A1W fragments
contain a considerable number of, sometimes highly nonconservative, amino acid replacements. In one of these species, the
ringneck parakeet (Psittacula krameri), the ATP5A1W gene is present in an inactive form because of the presence of a nonsense codon. Other changes, possibly leading
to an inactive ATP5A1W gene product, involve the substitution of arginine residues by cysteine in the ATP5A1W protein of the
mitred conure (Aratinga mitrata) and the blue and gold macaw (Ara ararauna). The data suggest also that although the divergence of the psittacine ATP5A1W and ATP5A1Z genes preceeded the origin of
the psittacidae, this divergence occurred independently of a similar process in the myna (Gracula religiosa), the outgroup used in this study.
Received: 6 September 2000 / Accepted: 7 March 2001 相似文献
13.
Capsular polysaccharides are important virulence factors both in Gram-positive and Gram-negative bacteria. A similar cluster
organization of the genes involved in the synthesis of bacterial exopolysaccharides has been postulated in both cases, suggesting
that these clusters evolved by module assembly. Horizontal gene transfer has been postulated to explain the polymorphism found
in these cellular polymers. The cap1K and cap3A genes coding for the pneumococcal type 1 and type 3 UDP-glucose dehydrogenases, respectively, have been compared with other
UDP-sugar dehydrogenases. We have observed that the evolutionary distance between Cap1K and Cap3A is approximately equal to
that found between Cap1K (or Cap3A) and other UDP-GlcDH of families evolutionarily distant like KfiD, the dehydrogenase from
Escherichia coli K5. On the basis of comparisons of G + C content, patterns of synonymous and nonsynonymous substitutions, dinucleotide frequencies,
and codon usage bias, we conclude that the kfiD gene has been introduced into E. coli from an exogenous source, probably from a streptococcal species.
Received: 26 May 1997 / Accepted: 30 July 1997 相似文献
14.
15.
Shuji Shigenobu Hidemi Watanabe Yoshiyuki Sakaki Hajime Ishikawa 《Journal of molecular evolution》2001,53(4-5):377-386
Endosymbiotic bacteria live in animal cells and are transmitted vertically at the time of the host's reproduction. In view
of their small and asexual populations with infrequent chances of recombination, these endocellular bacteria are expected
to accumulate mildly deleterious mutations. Previous studies showed that the DNA sequences of these bacteria evolved faster
than those of free-living bacteria. In this study, we compared all the ORFs of Buchnera, an endocellular bacterial symbiont of aphids, with those of 34 other prokaryotic organisms and estimated the effect of the
accelerated evolution of Buchnera on the functions of its proteins. It was revealed that Buchnera proteins contain many mutations at the sites where sequences are conserved in their orthologues in many other organisms.
In addition, amino acid replacements at the conserved sites are mostly changes to physicochemically different amino acids.
These results suggest that functions and conformations of Buchnera proteins have been seriously impaired or strongly modified. Indeed, extensive loss of functional motifs was observed in some
Buchnera proteins. In many Buchnera proteins mutations were not detected evenly throughout each molecule but tended to accumulate in some functional units, possibly
leading to loss of specific functions. As Buchnera has an unusual and limited gene repertory, it is conceivable that the manner of interactions among its proteins has been
changed, and thus, functional constraints over their amino acid residues have also been changed during evolution. This may
account for the loss of some functional units only in the Buchnera proteins. We obtained evidence that amino acid replacements in Buchnera were not always deleterious, but neutral or, in some cases, even positively selected.
Received: 14 December 2000 / Accepted: 12 March 2001 相似文献
16.
To study the evolution of human X-linked red and green opsin genes, genomic sequences in large regions of the two genes were
compared. The divergences in introns 3, 4, and 5 and the 3′ flanking sequence of the two genes are significantly lower than
those in exons 4 and 5. The homogenization mechanism of introns and the 3′ flanking sequence of human red and green opsin
genes is probably gene conversion, which also occurred in exons 1 and 6. At least one gene conversion event occurred in each
of three regions (1, 3, and 5) in the sequences compared. In conclusion, gene conversion has occurred frequently between human
red and green opsin genes, but exons 2, 3, 4, and 5 have been maintained distinct between the two genes by natural selection.
Received: 29 September 1997 / Accepted: 29 September 1997 相似文献
17.
18.
Lynne E. Vinall Alexander S. Hill Pascal Pigny Wendy S. Pratt Neil Toribara James R. Gum Young S. Kim Nicole Porchet Jean-Pierre Aubert D. M. Swallow 《Human genetics》1998,102(3):357-366
A family of four genes that encode major secreted mucins (MUC6, MUC2, MUC5AC and MUC5B) map to within 400kb on chromosome
11p15.5. These genes contain long stretches of tandem repeats of sequence that encode serine- and threonine-rich domains but
that otherwise show no similarity from gene to gene, and regions of unique sequence domains that do show evidence of sequence
homology. We have previously reported the existence of polymorphism in three of these genes but the extent and nature of this
allelic variation is now described here in detail. Variable number tandem repeat polymorphisms of MUC6, MUC2 and MUC5AC are
predicted to encode mucin polypeptides that differ in length. In the case of MUC2 and MUC6 these length differences are substantial
(up to twofold). MUC5B in contrast does not show common allele length variation. Three MUC2 mutations are reported, none of
which are associated with the meiotic recombinations previously observed in this region of chromosome 11.
Received: 24 July 1997 / Accepted: 13 November 1997 相似文献
19.
Gerhard Schenk Roy Layfield Judith M. Candy Ronald G. Duggleby Peter F. Nixon 《Journal of molecular evolution》1997,44(5):552-572
Members of the transketolase group of thiamine-diphosphate-dependent enzymes from 17 different organisms including mammals,
yeast, bacteria, and plants have been used for phylogenetic reconstruction. Alignment of the amino acid and DNA sequences
for 21 transketolase enzymes and one putative transketolase reveals a number of highly conserved regions and invariant residues
that are of predicted importance for enzyme activity, based on the crystal structure of yeast transketolase. One particular
sequence of 36 residues has some similarities to the nucleotide-binding motif and we designate it as the transketolase motif.
We report further evidence that the recP protein from Streptococcus pneumoniae might be a transketolase and we list a number of invariant residues which might be involved in substrate binding. Phylogenies
derived from the nucleotide and the amino acid sequences by various methods show a conventional clustering for mammalian,
plant, and gram-negative bacterial transketolases. The branching order of the gram-positive bacteria could not be inferred
reliably. The formaldehyde transketolase (sometimes known as dihydroxyacetone synthase) of the yeast Hansenula polymorpha appears to be orthologous to the mammalian enzymes but paralogous to the other yeast transketolases. The occurrence of more
than one transketolase gene in some organisms is consistent with several gene duplications. The high degree of similarity
in functionally important residues and the fact that the same kinetic mechanism is applicable to all characterized transketolase
enzymes is consistent with the proposition that they are all derived from one common ancestral gene. Transketolase appears
to be an ancient enzyme that has evolved slowly and might serve as a model for a molecular clock, at least within the mammalian
clade.
Received: 13 September 1995 / Accepted: 14 November 1996 相似文献