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1.
Marín I Fares MA González-Candelas F Barrio E Moya A 《Journal of molecular evolution》2001,52(1):17-28
We describe a new procedure to determine whether regional alterations in the evolutionary constraints imposed on paralogous
proteins have occurred. We used as models the A and B (alternatively called α and β) subunits of V/F/A-ATPases, originated
by a gene duplication more than 3 billion years ago. Changes associated to three major splits (eubacteria versus Archaea-eukaryotes;
Archaea versus eukaryotes; and among free-living bacteria and symbiotic mitochondria) were studied. Only in the first case,
when we compared eubacterial or mitochondrial F-ATPases versus eukaryotic vacuolar V-ATPases or archaeal A-ATPases, constraint
changes were observed. Modifications in the degree of regional constraining were not detected for the other two types of comparisons
(V-ATPases versus A-ATPases and within F-ATPases, respectively). When the rates of evolution of the two subunits were compared,
it was found that F-ATPases regulatory subunits evolved faster than catalytic subunits, but the opposite was true for A- and
V-ATPases. Our results suggest that, even for universal and essential proteins, selective constraints may be occasionally
altered. On the other hand, in some cases no changes were detected after periods of more than 2.2 billion years.
Received: 24 February 2000 / Accepted: 12 August 2000 相似文献
2.
Anton Karabinos Debashish Bhattacharya Hartmut D. Kratzin Norbert Hilschmann 《Journal of molecular evolution》1998,46(3):327-333
The human protein NEFA binds calcium, contains a leucine zipper repeat that does not form a homodimer, and is proposed (along
with the homologous Nuc protein) to have a common evolutionary history with an EF-hand ancestor. We have isolated and characterized
the N-terminal domain of NEFA that contains a signal sequence inferred from both endoproteinase Asp-N (Asp-N) and tryptic
digests. Analysis of this N-terminal sequence shows significant similarity to the conserved multiple domains of the mitochondrial
carrier family (MCF) proteins. The leader sequence of Nuc is, however, most similar to the signal sequences of membrane and/or
secreted proteins (e.g., mouse insulin-like growth factor receptor). We suggest that the divergent NEFA and Nuc N-terminal
sequences may have independent origins and that the common high hydrophobicity governs their targeting to the ER. These results
provide insights into signal sequence evolution and the multiple origins of protein targeting.
Received: 20 February 1997 / Accepted: 28 July 1997 相似文献
3.
4.
Yuji Inagaki Yasuko Hayashi-Ishimaru Megumi Ehara Ikuo Igarashi Takeshi Ohama 《Journal of molecular evolution》1997,45(3):295-300
The chloroplasts of euglenophytes and dinoflagellates have been suggested to be the vestiges of endosymbiotic algae acquired
during the process of evolution. However, the evolutionary positions of these organisms are still inconclusive, and they have
been tentatively classified as both algae and protozoa. A representative gene of the mitochondrial genome, cytochrome oxidase
subunit I (coxI), was chosen and sequenced to clarify the phylogenetic positions of four dinoflagellates, two euglenophytes and one apicomplexan
protist. This is the first report of mitochondrial DNA sequences for dinoflagellates and euglenophytes. Our COXI tree shows clearly that dinoflagellates are closely linked to apicomplexan parasites but not with algae. Euglenophytes and
algae appear to be only remotely related, with euglenophytes sharing a possible evolutionary link with kinetoplastids. The
COXI tree is in general agreement with the tree based on the nuclear encoded small subunit of ribosomal RNA (SSU rRNA) genes,
but conflicts with that based on plastid genes. These results support the interpretation that chloroplasts present in euglenophytes
and dinoflagellates were captured from algae through endosymbioses, while their mitochondria were inherited from the host
cell. We suggest that dinoflagellates and euglenophytes were originally heterotrophic protists and that their chloroplasts
are remnants of endosymbiotic algae.
Received: 24 March 1997 / Accepted: 21 April 1997 相似文献
5.
Nuria Saperas Manel Chiva David C. Pfeiffer Harold E. Kasinsky Juan Ausió 《Journal of molecular evolution》1997,44(4):422-431
We have characterized for the first time SNBPs from the hagfish Eptatratus stouti (Myxini) and the lamprey Lampetra tridentatus (Cephalaspidomorphi) and have found that histones are the major protein components of the sperm of these agnathans. We have
also conducted a systematic analysis of SNBPs from different groups of chondrichthyan fishes, including the skate Raja rhina and seven species of sharks. Together with our previous data showing the sporadic nature of SNBP evolution in bony fish (Saperas,
N., Ausio, J., Lloris, D. and Chiva, M. [1994] J. Mol. Evol. 39: 282–295), the present study provides a unique insight into the overall evolutionary complexity and variability of the
nuclear sperm proteins of fishes. It would appear that despite the discontinuous evolution of these proteins, the macroevolutionary
pattern of histone (H type) → protamine-like (PL type) → protamine (P type) has been conserved in fish evolution, as it has
in the evolution of other Deuterostomes.
Received: 11 June 1996 / Accepted: 6 August 1996 相似文献
6.
Nuclear and Nucleomorph SSU rDNA Phylogeny in the Cryptophyta and the Evolution of Cryptophyte Diversity 总被引:5,自引:0,他引:5
The plastid-bearing members of the Cryptophyta contain two functional eukaryotic genomes of different phylogenetic origin,
residing in the nucleus and in the nucleomorph, respectively. These widespread and diverse protists thus offer a unique opportunity
to study the coevolution of two different eukaryotic genomes within one group of organisms. In this study, the SSU rRNA genes
of both genomes were PCR-amplified with specific primers and phylogenetic analyses were performed on different data sets using
different evolutionary models. The results show that the composition of the principal clades obtained from the phylogenetic
analyses of both genes was largely congruent, but striking differences in evolutionary rates were observed. These affected
the topologies of the nuclear and nucleomorph phylogenies differently, resulting in long-branch attraction artifacts when
simple evolutionary models were applied. Deletion of long-branch taxa stabilized the internal branching order in both phylogenies
and resulted in a completely resolved topology in the nucleomorph phylogeny. A comparison of the tree topologies derived from
SSU rDNA sequences with characters previously used in cryptophyte systematics revealed that the biliprotein type was congruent,
but the type of inner periplast component incongruent, with the molecular trees. The latter is indicative of a hidden cellular
dimorphism (cells with two periplast types present in a single clonal strain) of presumably widespread occurrence throughout
cryptophyte diversity, which, in consequence, has far-reaching implications for cryptophyte systematics as it is practiced
today. 相似文献
7.
Naruo Nikoh Naoyuki Iwabe Kei-ichi Kuma Mutsuhito Ohno Tsutomu Sugiyama Yoko Watanabe Kinya Yasui Zhang Shi-cui Katsuji Hori Yoshiro Shimura Takashi Miyata 《Journal of molecular evolution》1997,45(1):97-106
Previously we suggested that four proteins including aldolase and triose phosphate isomerase (TPI) evolved with approximately
constant rates over long periods covering the whole animal phyla. The constant rates of aldolase and TPI evolution were reexamined
based on three different models for estimating evolutionary distances. It was shown that the evolutionary rates remain essentially
unchanged in comparisons not only between different classes of vertebrates but also between vertebrates and arthropods and
even between animals and plants, irrespective of the models used. Thus these enzymes might be useful molecular clocks for
inferring divergence times of animal phyla. To know the divergence time of Parazoa and Eumetazoa and that of Cephalochordata
and Vertebrata, the aldolase cDNAs from Ephydatia fluviatilis, a freshwater sponge, and the TPI cDNAs from Ephydatia fluviatilis and Branchiostoma belcheri, an amphioxus, have been cloned and sequenced. Comparisons of the deduced amino acid sequences of aldolase and TPI from the
freshwater sponge with known sequences revealed that the Parazoa–Eumetazoa split occurred about 940 million years ago (Ma)
as determined by the average of two proteins and three models. Similarly, the aldolase and TPI clocks suggest that vertebrates
and amphioxus last shared a common ancestor around 700 Ma and they possibly diverged shortly after the divergence of deuterostomes
and protostomes. 相似文献
8.
Michael Wallis 《Journal of molecular evolution》2001,53(1):10-18
Pituitary growth hormone (GH) and prolactin have been shown previously to display a pattern of evolution in which episodes
of rapid change are imposed on a low underlying basal rate (near-stasis). This study was designed to explore whether a similar
pattern is seen in the evolution of other protein hormones in mammals. Seven protein hormones were examined (with the common
α-subunit of the glycoprotein hormones providing an additional polypeptide for analysis)—those for which sequences from at
least four eutherian orders are available with a suitable non-eutherian outgroup. Six of these (GH, prolactin, insulin, parathyroid
hormone, glycoprotein hormone α-subunit, and luteinizing hormone β-subunit) showed markedly variable evolutionary rates in
each case with a pattern of a slow basal rate and bursts of rapid change, the precise positions of the bursts varying from
protein to protein. Two protein hormones (follicle-stimulating hormone β-subunit and thyroid-stimulating hormone β-subunit)
showed no significant rate variation. Based on the sequences currently available, and pooling data from all eight proteins,
the phase of slow basal change occupied about 85% of the sampled evolutionary time, but most evolutionary change (about 62%
of the substitutions accepted) occurred during the episodes of rapid change. It is concluded that, in mammals at least, a
pattern of prolonged periods of near-stasis with occasional episodes of rapid change provides a better model of evolutionary
change for protein hormones than the one of constant evolutionary rates that is commonly favored. The mechanisms underlying
this episodic evolution are not yet clear, and it may be that they vary from one group to another; in some cases, positive
selection appears to underlie bursts of rapid change. Where gene duplication is associated with a period of accelerated evolution
this often occurs at the end rather than the beginning of the episode. To what extent the type of pattern seen for protein
hormones can be extended to other proteins remains to be established.
Received: 10 October 2000 / Accepted: 18 December 2000 相似文献
9.
Complete sequences of mitochondrial DNA (mtDNA) are useful for the reconstruction of phylogenetic trees of mammals and, in
particular, for inferring higher-order relationships in mammals. In this study, we determined the complete sequence (16,705
bp) of the mtDNA of a Japanese megabat, the Ryukyu flying fox (Pteropus dasymallus). We analyzed this sequence phylogenetically by comparing it with the complete sequence of mtDNAs of 35 mammals in an effort
to reevaluate the enigmatic relationship between Megachiroptera and Microchiroptera and the relationships between them and
other mammals. Maximum-likelihood analysis of 12 concatenated mitochondrial proteins from 36 mammals strongly suggested the
monophyly of the order Chiroptera and its close relationship to Fereuungulata (Carnivora + Perissodactyla + Cetartiodactyla).
We estimated that megabats and microbats diverged approximately 58 MyrBP and discussed the origin and early evolution of Chiroptera
based on our findings.
Received: 28 January 2000 / Accepted: 30 June 2000 相似文献
10.
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
11.
Nucleotide Substitution Rate of Mammalian Mitochondrial Genomes 总被引:22,自引:0,他引:22
We present here for the first time a comprehensive study based on the analysis of closely related organisms to provide an
accurate determination of the nucleotide substitution rate in mammalian mitochondrial genomes. This study examines the evolutionary
pattern of the different functional mtDNA regions as accurately as possible on the grounds of available data, revealing some
important ``genomic laws.' The main conclusions can be summarized as follows. (1) High intragenomic variability in the evolutionary
dynamic of mtDNA was found. The substitution rate is strongly dependent on the region considered, and slow- and fast-evolving
regions can be identified. Nonsynonymous sites, the D-loop central domain, and tRNA and rRNA genes evolve much more slowly
than synonymous sites and the two peripheral D-loop region domains. The synonymous rate is fairly uniform over the genome,
whereas the rate of nonsynonymous sites depends on functional constraints and therefore differs considerably between genes.
(2) The commonly accepted statement that mtDNA evolves more rapidly than nuclear DNA is valid only for some regions, thus
it should be referred to specific mitochondrial components. In particular, nonsynonymous sites show comparable rates in mitochondrial
and nuclear genes; synonymous sites and small rRNA evolve about 20 times more rapidly and tRNAs about 100 times more rapidly
in mitochondria than in their nuclear counterpart. (3) A species-specific evolution is particularly evident in the D-loop
region. As the divergence times of the organism pairs under consideration are known with sufficient accuracy, absolute nucleotide
substitution rates are also provided.
Received: 11 May 1998 / Accepted: 2 September 1998 相似文献
12.
The Path from the RNA World 总被引:1,自引:0,他引:1
We describe a sequential (step by step) Darwinian model for the evolution of life from the late stages of the RNA world through
to the emergence of eukaryotes and prokaryotes. The starting point is our model, derived from current RNA activity, of the
RNA world just prior to the advent of genetically-encoded protein synthesis. By focusing on the function of the protoribosome
we develop a plausible model for the evolution of a protein-synthesizing ribosome from a high-fidelity RNA polymerase that
incorporated triplets of oligonucleotides. With the standard assumption that during the evolution of enzymatic activity, catalysis
is transferred from RNA → RNP → protein, the first proteins in the ``breakthrough organism' (the first to have encoded protein
synthesis) would be nonspecific chaperone-like proteins rather than catalytic. Moreover, because some RNA molecules that pre-date
protein synthesis under this model now occur as introns in some of the very earliest proteins, the model predicts these particular
introns are older than the exons surrounding them, the ``introns-first' theory. Many features of the model for the genome
organization in the final RNA world ribo-organism are more prevalent in the eukaryotic genome and we suggest that the prokaryotic
genome organization (a single, circular genome with one center of replication) was derived from a ``eukaryotic-like' genome
organization (a fragmented linear genome with multiple centers of replication). The steps from the proposed ribo-organism
RNA genome → eukaryotic-like DNA genome → prokaryotic-like DNA genome are all relatively straightforward, whereas the transition
prokaryotic-like genome → eukaryotic-like genome appears impossible under a Darwinian mechanism of evolution, given the assumption
of the transition RNA → RNP → protein. A likely molecular mechanism, ``plasmid transfer,' is available for the origin of
prokaryotic-type genomes from an eukaryotic-like architecture. Under this model prokaryotes are considered specialized and
derived with reduced dependence on ssRNA biochemistry. A functional explanation is that prokaryote ancestors underwent selection
for thermophily (high temperature) and/or for rapid reproduction (r selection) at least once in their history.
Received: 14 January 1997 / Accepted: 19 May 1997 相似文献
13.
Jen-Jen Lin Tzung-Horng Yang Benjamin D. Wahlstrand Peter A. Fields George N. Somero 《Journal of molecular evolution》2002,54(1):107-117
Unlike birds and mammals, teleost fish express two paralogous isoforms (paralogues) of cytosolic malate dehydrogenase (cMDH;
EC 1.1.1.37; NAD+: malate oxidoreductase) whose evolutionary relationships to the single cMDH of tetrapods are unknown. We sequenced complementary
DNAs for both cMDHs and the mitochondrial isoform (mMDH) of the fish Sphyraena idiastes (south temperate barracuda) and compared the sequences, kinetic properties, and thermal stabilities of the three isoforms
with those of mammalian orthologues. Both fish cMDHs comprise 333 residues and have subunit masses of approximately 36 kDa.
One cytosolic isoform, cMDH-S, was significantly more heat-stable than either the other cMDH (cMDH-L) or mMDH. In contradiction
to the generally accepted model of vertebrate cMDH evolution, our phylogenetic analysis indicates that the duplication of
the fish cytosolic paralogues occurred after the divergence of the lineages leading to teleosts and tetrapods. cMDH-L and
cMDH-S differed in optimal concentrations of substrates and cofactors and apparent Michaelis–Menten constants, suggesting
that the two paralogues may play distinct physiological roles. Differences in intrinsic thermal stability among MDH paralogues
may reflect different degrees of stabilization in vivo by extrinsic stabilizers, notably protein concentration in the case
of mMDH. Thermal stabilities of porcine mMDH and cMDH-L, but not cMDH-S, were significantly increased when denaturation was
measured at a high protein (bovine serum albumin; BSA) concentration, but the BSA-induced stabilization reduced the catalytic
activity.
Received: 5 April 2001 / Accepted: 28 June 2001 相似文献
14.
If lateral gene transfer (LGT) has affected all genes over the course of prokaryotic evolution, reconstruction of organismal
phylogeny is compromised. However, if a core of genes is immune to transfer, then the evolutionary history of that core might
be our most reliable guide to the evolution of organisms. Such a core should be preferentially included in the subset of genes
shared by all organisms, but where universally conserved genes have been analyzed, there is too little phylogenetic signal
to allow determination of whether or not they indeed have the same history (Hansmann and Martin 2000; Teichmann and Mitchison
1999). Here we look at a more restricted set, 521 homologous genes (COGs) simultaneously present in four sequenced euryarchaeal
genomes. Although there is overall little robust phylogenetic signal in this data set, there is, among well-supported trees,
strong representation of all three possible four-taxon topologies. ``Informational' genes seem no less subject to LGT than
are ``operational genes,' within the euryarchaeotes. We conclude that (i) even in this collection of conserved genes there
has been extensive LGT (orthologous gene replacement) and (ii) the notion that there is a core of nontransferable genes (the
``core hypothesis') has not been proven and may be unprovable.
Received: 7 November 2000 / Accepted: 20 February 2001 相似文献
15.
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
16.
Evolution of the 14-3-3 Protein Family: Does the Large Number of Isoforms in Multicellular Organisms Reflect Functional Specificity? 总被引:1,自引:0,他引:1
Rosenquist M Sehnke P Ferl RJ Sommarin M Larsson C 《Journal of molecular evolution》2000,51(5):446-458
14-3-3 proteins constitute a family of eukaryotic proteins that are key regulators of a large number of processes ranging
from mitosis to apoptosis. 14-3-3s function as dimers and bind to particular motifs in their target proteins. To date, 14-3-3s
have been implicated in regulation or stabilization of more than 35 different proteins. This number is probably only a fraction
of the number of proteins that 14-3-3s bind to, as reports of new target proteins have become more frequent. An examination
of 14-3-3 entries in the public databases reveals 153 isoforms, including alleloforms, reported in 48 different species. The
number of isoforms range from 2, in the unicellular organism Saccharomyces cerevisiae, to 12 in the multicellular organism Arabidopsis thaliana. A phylogenetic analysis reveals that there are four major evolutionary lineages: Viridiplantae (plants), Fungi, Alveolata,
and Metazoa (animals). A close examination of the aligned amino acid sequences identifies conserved amino acid residues and
regions of importance for monomer stabilization, dimer formation, target protein binding, and the nuclear export function.
Given the fact that 53% of the protein is conserved, including all amino acid residues in the target binding groove of the
14-3-3 monomer, one might expect little to no isoform specificity for target protein binding. However, using surface plasmon
resonance we show that there are large differences in affinity between nine 14-3-3 isoforms of A. thaliana and a target peptide representing a novel binding motif present in the C terminus of the plant plasma membrane H+ATPase. Thus, our data suggest that one reason for the large number of isoforms found in multicellular organisms is isoform-specific
functions.
Received: 19 April 2000 / Accepted: 24 July 2000 相似文献
17.
A.D. Shutov H. Braun Yu.V. Chesnokov Ch. Horstmann I.A. Kakhovskaya H. Bäumlein 《Journal of molecular evolution》1998,47(4):486-492
The development of seeds as a specialized organ for the nutrition, protection, and dispersal of the next generation was an
important step in the evolution of land plants. Seed maturation is accompanied by massive synthesis of storage compounds such
as proteins, starch, and lipids. To study the processes of seed storage protein evolution we have partially sequenced storage
proteins from maturing seeds of representatives from the gymnosperm genera Gnetum, Ephedra, and Welwitschia—morphologically diverse and unusual taxa that are grouped in most formal systems into the common order Gnetales. Based on
partial N-terminal amino acid sequences, oligonucleotide primers were derived and used for PCR amplification and cloning of
the corresponding cDNAs. We also describe the structure of the nuclear gene for legumin of Welwitschia mirabilis. This first gnetalean nuclear gene structure contains introns in only two of the four conserved positions previously characterized
in other spermatophyte legumin genes. The distinct phylogenetic status of the gnetalean taxa is also reflected in a sequence
peculiarity of their legumin genes. A comparative analysis of exon/intron sequences leads to the hypothesis that legumin genes
from Gnetales belong to a monophyletic evolutionary branch clearly distinct from that of legumin genes of extant Ginkgoales
and Coniferales as well as from all angiosperms.
Received: 5 June 1997 / Accepted: 31 March 1998 相似文献
18.
Fungi have evolved a unique α-aminoadipate pathway for lysine biosynthesis. The fungal-specific enzyme homoaconitate hydratase
from this pathway is moderately similar to the aconitase-family proteins from a diverse array of taxonomic groups, which have
varying modes of obtaining lysine. We have used the similarity of homoaconitate hydratase to isopropylmalate isomerase (serving
in leucine biosynthesis), aconitase (from the tricarboxylic acid cycle), and iron-responsive element binding proteins (cytosolic
aconitase) from fungi and other eukaryotes, eubacteria, and archaea to evaluate possible evolutionary scenarios for the origin
of this pathway. Refined sequence alignments show that aconitase active site residues are highly conserved in each of the
enzymes, and intervening sequence sites are quite dissimilar. This pattern suggests strong purifying selection has acted to
preserve the aconitase active site residues for a common catalytic mechanism; numerous other substitutions occur due to adaptive
evolution or simply lack of functional constraint. We hypothesize that the similarities are the remnants of an ancestral gene
duplication, which may not have occurred within the fungal lineage. Maximum likelihood, neighbor joining, and maximum parsimony
phylogenetic comparisons show that the α-aminoadipate pathway enzyme is an outgroup to all aconitase family proteins for which
sequence is currently available.
Received: 7 October 1997 相似文献
19.
We studied 10 protein-coding mitochondrial genes from 19 mammalian species to evaluate the effects of 10 amino acid properties
on the evolution of the genetic code, the amino acid composition of proteins, and the pattern of nonsynonymous substitutions.
The 10 amino acid properties studied are the chemical composition of the side chain, two polarity measures, hydropathy, isoelectric
point, volume, aromaticity, aliphaticity, hydrogenation, and hydroxythiolation. The genetic code appears to have evolved toward
minimizing polarity and hydropathy but not the other seven properties. This can be explained by our finding that the presumably
primitive amino acids differed much only in polarity and hydropathy, but little in the other properties. Only the chemical
composition (C) and isoelectric point (IE) appear to have affected the amino acid composition of the proteins studied, that
is, these proteins tend to have more amino acids with typical C and IE values, so that nonsynonymous mutations tend to result
in small differences in C and IE. All properties, except for hydroxythiolation, affect the rate of nonsynonymous substitution,
with the observed amino acid changes having only small differences in these properties, relative to the spectrum of all possible
nonsynonymous mutations.
Received: 2 January 1998 / Accepted: 25 April 1998 相似文献
20.
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