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1.
Joachim Schütze Alexander Skorokhod Isabel M. Müller Werner E.G. Müller 《Journal of molecular evolution》2001,53(4-5):402-415
One crucial event during evolution to multicellularity was the development of either direct cell–cell contact or indirect
interaction via extracellular matrix (ECM) molecules. The identification of those polypeptides provides conclusive data on
the phylogenetic relationship of metazoan phyla and helps us to understand the position of the Metazoa among the other kingdoms.
Recently it became evident that the ECM of sponges is amazingly complex; it is composed of fibrous molecules, e.g., collagen,
and their corresponding receptors, which are highly similar to those existing in other metazoan phyla. While these data already
support the view of monophyly of Metazoa, additional studies are required to understand whether these molecules, which are
similar in their primary sequence, also have the same function throughout the metazoan kingdom. In the present study we identified
the ligand for one of the autopomorphic characters of Metazoa, the single-transmembrane receptor protein with the receptor
tyrosine kinase (RTK) from G. cydonium, as an example: the putative mucus-like protein from G. cydonium. This protein was upregulated during autograft fusion in the homologous system with kinetics similar to those of the RTK.
Additionally, a cDNA was isolated from S. domuncula whose deduced polypeptide displays a high sequence similarity to dermatopontin, an ECM molecule found exclusively in Metazoa.
Furthermore, it is documented that expression of the fibrous ECM molecule collagen is regulated by the characteristic metazoan
morphogens myotrophin and endothelial monocyte-activating polypeptide. These data indicate that the ECM of sponges is not
an unstructured ground substance but provides the basis for integrated cell communication.
Received: 26 October 2000 / Accepted: 1 February 2001 相似文献
2.
Vera Gamulin Alexander Skorokhod Vadim Kavsan Isabel M. Müller Werner E. G. Müller 《Journal of molecular evolution》1997,44(3):242-252
We have analyzed the gene that encodes receptor tyrosine kinase (RTK) from the marine sponge Geodia cydonium, which belongs to the most ancient and simple metazoan groups, the Porifera. RTKs are enzymes found only in metazoa. The sponge
gene contains two introns in the extracellular part of the protein. However, the rest of the protein (transmembrane and intracellular
part), including the tyrosine kinase (TK)-domain, is encoded by a single exon. In contrast, all TK genes, so far known only
from higher animals (vertebrates), contain several introns especially in the TK-domain. The TK-domain of G. cydonium shows similarity with numerous members of receptor as well as nonreceptor TKs. Phylogenetic analysis of the sponge TK-domain
indicates that this enzyme branched off first from the common tree of metazoan TK proteins. Consequently, we assume that introns,
found in the TK-domains of genes from higher animals, were inserted into these genes after splitting off the sponge taxa from
other metazoan organisms (over 600 million years ago). Our results support the view that ancient genes were not ``in pieces.'
Received: 8 August 1996 / Accepted: 4 November 1996 相似文献
3.
4.
Michael Kruse Vera Gamulin Helena Cetkovic Zeev Pancer Isabel M. Müller Werner E. G. Müller 《Journal of molecular evolution》1996,43(4):374-383
Protein kinases C (PKCs) comprise closely related Ser/Thr kinases, ubiquitously present in animal tissues; they respond to
second messengers, e.g., Ca2+ and/or diacylglycerol, to express their activities. Two PKCs have been sequenced from Geodia cydonium, a member of the lowest multicellular animals, the sponges (Porifera). One sponge G. cydonium PKC, GCPKC1, belongs to the ``novel' (Ca2+-independent) PKC (nPKC) subfamily while the second one, GCPKC2, has the hallmarks of the ``conventional' (Ca2+-dependent) PKC (cPKC) subfamily. The alignment of the Ser/Thr catalytic kinase domains, of the predicted aa sequences for
these cDNAs with respective segments from previously reported sequences, revealed highest homology to PKCs from animals but
also distant relationships to Ser/Thr kinases from protozoa, plants, and bacteria. However, a comparison of the complete structures
of the sponge PKCs, which are—already—identical to those of nPKCs and cPKCs from higher metazoa, with the structures of protozoan,
plant, and bacterial Ser/Thr kinases indicates that the metazoan PKCs have to be distinguished from the nonmetazoan enzymes.
These data indicate that metazoan PKCs have a universal common ancestor which they share with the nonmetazoan Ser/Thr kinases
with respect to the kinase domain, but they differ from them in overall structural composition.
Received: 10 January 1996 / Accepted: 12 March 1996 相似文献
5.
Phylogenetic Analysis of Invertebrate Lysozymes and the Evolution of Lysozyme Function 总被引:22,自引:0,他引:22
Bachali S Jager M Hassanin A Schoentgen F Jollès P Fiala-Medioni A Deutsch JS 《Journal of molecular evolution》2002,54(5):652-664
We isolated and sequenced the cDNAs coding for lysozymes of six bivalve species. Alignment and phylogenetic analysis showed
that, together with recently described bivalve lysozymes, the leech destabilase, and a number of putative proteins from extensive
genomic and cDNA analyses, they belong to the invertebrate type of lysozymes (i type), first described by Jollès and Jollès
(1975). We determined the genomic structure of the gene encoding the lysozyme of Mytilus edulis, the common mussel. We provide evidence that the central exon of this gene is homologous to the second exon of the chicken
lysozyme gene, belonging to the c type. We propose that the origin of this domain can be traced back in evolution to the origin
of bilaterian animals. Phylogenetic analysis suggests that i-type proteins form a monophyletic family.
Received: 21 May 2001 / Accepted: 22 October 2001 相似文献
6.
7.
The recent completion of the sequencing of the Saccharomyces cerevisiae genome provides a unique opportunity to analyze the evolutionary relationships existing among the entire complement of retrotransposons
residing within a single genome. In this article we report the results of such an analysis of two closely related families
of yeast long terminal repeat (LTR) retrotransposons, Ty1 and Ty2. In our study, we analyzed the molecular variation existing
among the 32 Ty1 and 13 Ty2 elements present within the S. cerevisiae genome recently sequenced within the context of the yeast genome project. Our results indicate that while the Ty1 family
is most likely ancestral to Ty2 elements, both families of elements are relatively recent components of the S. cerevisiae genome. Our results also indicate that both families of elements have been subject to purifying selection within their protein
coding regions. Finally, and perhaps most interestingly, our results indicate that a relatively recent recombination event
has occurred between Ty2 and a subclass of Ty1 elements involving the LTR regulatory region. We discuss the possible biological
significance of these findings and, in particular, how they contribute to a better overall understanding of LTR retrotransposon
evolution.
Received: 30 September 1997 / Accepted: 3 February 1998 相似文献
8.
Drosophila ananassae is known to produce numerous alpha-amylase variants. We have cloned seven different Amy genes in an African strain homozygous for the AMY1,2,3,4 electrophoretic pattern. These genes are organized as two main clusters:
the first one contains three intronless copies on the 2L chromosome arm, two of which are tandemly arranged. The other cluster,
on the 3L arm, contains two intron-bearing copies. The amylase variants AMY1 and AMY2 have been assigned to the intronless
cluster, and AMY3 and AMY4 to the second one. The divergence of coding sequences between clusters is moderate (6.1% in amino
acids), but the flanking regions are very different, which could explain their differential regulation. Within each cluster,
coding and noncoding regions are conserved. Two very divergent genes were also cloned, both on chromosome 3L, but very distant
from each other and from the other genes. One is the Amyrel homologous (41% divergent), the second one, Amyc1 (21.6% divergent) is unknown outside the D. ananassae subgroup. These two genes have unknown functions.
Received: 30 May 2000 / Accepted: 17 July 2000 相似文献
9.
Juan Ausiö Manfred L. J. Van Veghel Raquel Gomez Daniel Barreda 《Journal of molecular evolution》1997,45(1):91-96
We have isolated and characterized for the first time, the SNBPs from an organism (Neofibularia nolitangere) of the phylum Porifera (Sponges). We have shown that these proteins consist of histones which, as expected, exhibit an amino
acid composition very similar to that of other eukaryotic histones. The finding of histones in the sperm of these primitive
organisms provides support to the notion that histones (SNBPs of the histone, H, type) were the proteins present at the onset
of SNBP evolution. In contrast, a discrete number of alternative SNBP types (protamine-like, PL; protamine, P, types) seem
to have appeared later on in the course of evolution and are found in both protostomes and deuterostomes, most likely as a
result of processes of parallel evolution.
Received: 5 March 1997 / Accepted: 6 March 1997 相似文献
10.
11.
Barbara Blumbach Bärbel Diehl-Seifert Jürgen Seack Renate Steffen Isabel M. Müller W. E. G. Müller 《Immunogenetics》1999,49(9):751-763
A cDNA encoding a receptor tyrosine kinase (RTK) was previously cloned and expressed from the marine sponge (Porifera) Geodia cydonium. In addition to the two intracellular regions characteristic for RTKs, two immunoglobulin (Ig)-like domains are found in
the extracellular part of the sponge RTK. In the present study it is shown that no further Ig-like domain is present in the
upstream region of the cDNA as well as of the gene hitherto known from the sponge RTK. Two different full-length cDNAs have
been isolated and characterized in the present study, which possess two Ig-like domains, one transmembrane segment, and only
a short intracellular part, without a TK domain. The two deduced polypeptides were preliminarily termed sponge adhesion molecules
(SAM). The longer form of the SAM, GCSAML, encodes a deduced aa sequence, GCSAML, which comprises in the open reading frame 505 amino acids (aa) and has a calculated
M
r of 53911. The short form, GCSAMS, has 313 aa residues and an M
r of 33987. The two Ig-like domains in GCSAML and GCSAMS are highly similar to the corresponding Ig-like domains in the RTKs
from G. cydonium; the substitutions on both the aa and nt level are restricted to a few sites. Phylogenetic analyses revealed that the Ig-like
domain 1 is similar to the human Ig lambda chain variable region, while the Ig-like domain 2 is related more closely to the
human Ig heavy chain variable region. Transplantation experiments (autografting) were performed to demonstrate that the level
of expression of the two new genes, GCSAML and GCSAMS, is upregulated during the self/self fusion process. Immunohistochemical analyses using antibodies raised against the two
Ig-like domains demonstrate a strong expression in the fusion zone between graft and host. This finding has been supported
by northern blotting experiments that revealed that especially GCSAML is strongly upregulated after autografting (up to 12-fold); the expression of GCSAMS reaches a value of 5-fold if compared with the controls. The results presented here demonstrate that the expression of the
new molecules described, comprising two Ig-like domains, is upregulated during the process of autograft fusion.
Received: 17 November 1998 / Revised: 15 March 1999 相似文献
12.
We have determined the genomic structure of an integrin β-subunit gene from the coral, Acropora millepora. The coding region of the gene contains 26 introns, spaced relatively uniformly, and this is significantly more than have
been found in any integrin β-subunit genes from higher animals. Twenty-five of the 26 coral introns are also found in a β-subunit
gene from at least one other phylum, indicating that the coral introns are ancestral. While there are some suggestions of
intron gain or sliding, the predominant theme seen in the homologues from higher animals is extensive intron loss. The coral
baseline allows one to infer that a number of introns found in only one phylum of higher animals result from frequent intron
loss, as opposed to the seemingly more parsimonious alternative of isolated intron gain. The patterns of intron loss confirm
results from protein sequences that most of the vertebrate genes, with the exception of β4, belong to one of two β subunit
families. The similarity of the patterns within each of the β1,2,7 and β3,5,6,8 groups indicates that these gene structures
have been very stable since early vertebrate evolution. Intron loss has been more extensive in the invertebrate genes, and
obvious patterns have yet to emerge in this more limited data set.
Received: 5 March 2001 / Accepted: 17 May 2001 相似文献
13.
Wei Wu Morris Goodman Margaret I. Lomax Lawrence I. Grossman 《Journal of molecular evolution》1997,44(5):477-491
Cytochrome c oxidase (COX) is a multi-subunit enzyme complex that catalyzes the final step of electron transfer through the respiratory
chain on the mitochondrial inner membrane. Up to 13 subunits encoded by both the mitochondrial (subunits I, II, and III) and
nuclear genomes occur in eukaryotic organisms ranging from yeast to human. Previously, we observed a high number of amino
acid replacements in the human COX IV subunit compared to mouse, rat, and cow orthologues. Here we examined COX IV evolution
in the two groups of anthropoid primates, the catarrhines (hominoids, cercopithecoids) and platyrrhines (ceboids), as well
as one prosimian primate (lorisiform), by sequencing PCR-amplified portions of functional COX4 genes from genomic DNAs. Phylogenetic analysis of the COX4 sequence data revealed that accelerated nonsynonymous substitution rates were evident in the early evolution of both catarrhines
and, to a lesser extent, platyrrhines. These accelerated rates were followed later by decelerated rates, suggesting that positive
selection for adaptive amino acid replacement became purifying selection, preserving replacements that had occurred. The evidence
for positive selection was especially pronounced along the catarrhine lineage to hominoids in which the nonsynonymous rate
was first faster than the synonymous rate, then later much slower. The rates of three types of ``neutral DNA' nucleotide
substitutions (synonymous substitutions, pseudogene nucleotide substitutions, and intron nucleotide substitutions) are similar
and are consistent with previous observations of a slower rate of such substitutions in the nuclear genomes of hominoids than
in the nuclear genomes of other primate and mammalian lineages.
Received: 22 May 1996 / Accepted: 24 November 1996 相似文献
14.
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
15.
Isaäc J. Nijman Patrick van Tessel Johannes A. Lenstra 《Journal of molecular evolution》2002,54(1):9-16
SINE retrotransposition events have proven their value as phylogenetic markers in several eukaryotic taxa at different taxonomic
levels. The genomes of ruminants contain three related SINE elements, Bov-tA, Bov-A2, and Bov-B. To estimate the time points
of retrotransposition of individual copies of these SINEs, we designed PCR primers on database sequences containing SINE insertions
in cattle, sheep, or goat genomes and tested for the presence of these copies in the genomes of other ruminants. It was checked
by sequencing whether length variation of the PCR products reflected a SINE retrotransposition. One Bov-B and nine Bov-tA
insertions were shared by cattle, sheep, goat, and giraffe, indicating an early retrotransposition event before the radiation
of the Pecora, while three other Bov-tA and two Bov-B elements were apparently inserted later. The ruminant α-lactalbumine
gene contains a hotspot of early and more recent Bov-tA insertions, a Bov-tA replacement as well as a recent Bov-B insertion.
Three Bov-A2 insertions were found to be shared only by the Bovidae, the Bovini, and the Bos and Bison species, respectively, indicating that most Bov-A2 insertions are relatively recent. The time elapsed since the retrotransposition
was also reflected in the degeneration of the direct repeats that flank SINE inserts. We suggest that retrotransposition of
SINEs may serve as phylogenetic markers in the ruminant families, subfamilies, and even tribes. In addition, sequencing of
SINE insertions revealed several other unique deletions/insertions that also may be informative for phylogenetic reconstructions
of ruminants.
Received: 19 January 2001 / Accepted: 6 June 2001 相似文献
16.
Takehiro Kusakabe Isato Araki Noriyuki Satoh William R. Jeffery 《Journal of molecular evolution》1997,44(3):289-298
The origin and evolutionary relationship of actin isoforms was investigated in chordates by isolating and characterizing
two new ascidian cytoplasmic and muscle actin genes. The exon–intron organization and sequences of these genes were compared
with those of other invertebrate and vertebrate actin genes. The gene HrCA1 encodes a cytoplasmic (nonmuscle)-type actin, whereas the MocuMA2 gene encodes an adult muscle-type actin. Our analysis of these genes showed that intron positions are conserved among the
deuterostome actin genes. This suggests that actin gene families evolved from a single actin gene in the ancestral deuterostome.
Sequence comparisons and molecular phylogenetic analyses also suggested a close relationship between the ascidian and vertebrate
actin isoforms. It was also found that there are two distinct lineages of muscle actin isoforms in ascidians: the larval muscle
and adult body-wall isoforms. The four muscle isoforms in vertebrates show a closer relationship to each other than to the
ascidian muscle isoforms. Similarly, the two cytoplasmic isoforms in vertebrates show a closer relationship to each other
than to the ascidian and echinoderm cytoplasmic isoforms. In contrast, the two types of ascidian muscle actin diverge from
each other. The close relationship between the ascidian larval muscle actin and the vertebrate muscle isoforms was supported
by both neighbor-joining and maximum parsimony analyses. These results suggest that the chordate ancestor had at least two
muscle actin isoforms and that the vertebrate actin isoforms evolved after the separation of the vertebrates and urochordates.
Received: 20 June 1996 / Accepted: 16 October 1996 相似文献
17.
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
18.
Actin is a highly conserved protein although many isoforms exist. In vertebrates and insects the different actin isoforms
can be grouped by their amino acid sequence and tissue-specific gene expression into muscle and nonmuscle actins, suggesting
that the different actins may have a functional significance. We ask here whether atomic models for G- and F-actins may help
to explain this functional diversity. Using a molecular graphics program we have mapped the few amino acids that differ between
isoactins. A small number of residues specific for muscle actins are buried in internal positions and some present a remarkable
organization. Within the molecule, the replacements observed between muscle and nonmuscle actins are often accompanied by
compensatory changes. The others are dispersed on the protein surface, except for a cluster located at the N-terminus which
protrudes outward. Only a few of these residues specific for muscle actins are present in known ligand binding sites except
the N-terminus, which has a sequence specific for each isoactin and is directly implicated in the binding to myosin. When
we simulated the replacements of side chains of residues specific for muscle actins to those specific for nonmuscle actins,
the N-terminus appears to be less compact and more flexible in nonmuscle actins. This would represent the first conformational
grounds for proposing that muscle and nonmuscle actins may be functionally distinguishable. The rest of the molecule is very
similar or identical in all the actins, except for a possible higher internal flexibility in muscle actins. We propose that
muscle actin genes have evolved from genes of nonmuscle actins by substitutions leading to some conformational changes in
the protruding N-terminus and the internal dynamics of the main body of the protein.
Received: 15 March 1996 / Accepted: 14 July 1996 相似文献
19.
Evolution of Substrate Specificities in the P-Type ATPase Superfamily 总被引:23,自引:0,他引:23
P-type ATPases make up a large superfamily of ATP-driven pumps involved in the transmembrane transport of charged substrates.
We have performed an analysis of conserved core sequences in 159 P-type ATPases. The various ATPases group together in five
major branches according to substrate specificity, and not according to the evolutionary relationship of the parental species,
indicating that invention of new substrate specificities is accompanied by abrupt changes in the rate of sequence evolution.
A hitherto-unrecognized family of P-type ATPases has been identified that is expected to be represented in all the major phyla
of eukarya.
Received: 21 May 1997 / Accepted: 1 August 1997 相似文献
20.
Lucy C. Sullivan Christopher B. Daniels Ian D. Phillips Sandra Orgeig Jeffrey A. Whitsett 《Journal of molecular evolution》1998,46(2):131-138
Surface tension is reduced at the air–liquid interface in the lung by a mixture of lipids and proteins termed pulmonary surfactant.
This study is the first to provide evidence for the presence of a surfactant-specific protein (Surfactant Protein A—SP-A)
in the gas-holding structures of representatives of all the major vertebrate groups. Western blot analysis demonstrated cross-reactivity
between an antihuman SP-A antibody and material lavaged from lungs or swimbladders of members from all vertebrate groups.
Immunocytochemistry localized this SP-A–like protein to the air spaces of lungs from the actinopterygiian fish and lungfish.
Northern blot analysis indicated that regions of the mouse SP-A cDNA sequence are complementary to lung mRNA from all species
examined. The presence of an SP-A–like protein and SP-A mRNA in members of all the major vertebrate groups implies that the
surfactant system had a single evolutionary origin in the vertebrates. Moreover, the evolution of the surfactant system must
have been a prerequisite for the evolution of airbreathing. The presence of SP-A in the goldfish swimbladder demonstrates
a role for the surfactant system in an organ that is no longer used for airbreathing.
Received: 5 March 1997 / Accepted: 14 June 1997 相似文献