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1.
Soullier S Jay P Poulat F Vanacker JM Berta P Laudet V 《Journal of molecular evolution》1999,48(5):517-527
From a database containing the published HMG protein sequences, we constructed an alignment of the HMG box functional domain
based on sequence identity. Due to the large number of sequences (more than 250) and the short size of this domain, several
data sets were used. This analysis reveals that the HMG box superfamily can be separated into two clearly defined subfamilies:
(i) the SOX/MATA/TCF family, which clusters proteins able to bind to specific DNA sequences; and (ii) the HMG/UBF family,
which clusters members which bind non specifically to DNA. The appearance and diversification of these subfamilies largely
predate the split between the yeast and the metazoan lineages. Particular emphasis was placed on the analysis of the SOX subfamily.
For the first time our analysis clearly identified the SOX subfamily as structured in six groups of genes named SOX5/6, SRY,
SOX2/3, SOX14, SOX4/22, and SOX9/18. The validity of these gene clusters is confirmed by their functional characteristics
and their sequences outside the HMG box. In sharp contrast, there are only a few robust branching patterns inside the UBF/HMG
family, probably because of the much more ancient diversification of this family than the diversification of the SOX family.
The only consistent groups that can be detected by our analysis are HMG box 1, vertebrate HMG box 2, insect SSRP, and plant
HMG. The various UBF boxes cannot be clustered together and their diversification appears to be extremely ancient, probably
before the appearance of metazoans.
Received: 20 July 1998 / Accepted: 19 October 1998 相似文献
2.
Positive Darwinian Selection Promotes Heterogeneity Among Members of the Antifreeze Protein Multigene Family 总被引:9,自引:0,他引:9
A variety of organisms have independently evolved proteins exhibiting antifreeze activity that allows survival at subfreezing
temperatures. The antifreeze proteins (AFPs) bind ice nuclei and depress the freezing point by a noncolligative absorption–inhibition
mechanism. Many organisms have a heterogeneous suite of AFPs with variation in primary sequence between paralogous loci. Here,
we demonstrate that the diversification of the AFP paralogues is promoted by positive Darwinian selection in two independently
evolved AFPs from fish and beetle. First, we demonstrate an elevated rate of nonsynonymous substitutions compared to synonymous
substitutions in the mature protein coding region. Second, we perform phylogeny-based tests of selection to demonstrate a
subset of codons is subjected to positive selection. When mapped onto the three-dimensional structure of the fish antifreeze
type III antifreeze structure, these codons correspond to amino acid positions that surround but do not interrupt the putative
ice-binding surface. The selective agent may be related to efficient binding to diverse ice surfaces or some other aspect
of AFP function.
Received: 27 February 2001 / Accepted: 12 September 2001 相似文献
3.
Mirko Beljanski 《Journal of molecular evolution》1996,42(5):493-499
In the presence of Mg2+ ions, polynucleotide phosphorylase (PNPase, EC 2.7.7.8) is known to synthesize RNA-like polymers using ribonucleoside-5′-diphosphate
(NDP) substrates but to be unable to utilize deoxyribonucleoside substrates. Our experiments show that when MgCl2 is replaced by FeCl3, PNPase becomes able to synthesize deoxyheteropolymers using deoxyribonucleoside-5′-diphosphates (dNDPs). The deoxyheteropolymer
formed from the four dNDPs is degraded by pancreatic DNase, but not by RNase, and is readily used as a template by DNA-dependent
DNA polymerase. Synthesis of this DNA-like polymer is accomplished de novo without the help of any primer or preexisting template.
What is more, dA/dG and dC/dT ratios of polymers synthesized by different bacterial PNPases closely match ratios found in
DNA of the bacterial species the enzyme came from. 相似文献
4.
5.
6.
Regulation of Na-K-ATPase Activity in the Proximal Tubule: Role of the Protein Kinase C Pathway and of Eicosanoids 总被引:4,自引:0,他引:4
To evaluate further the signal transduction mechanisms involved in the short-term modulation of Na-K-ATPase activity in the
mammalian kidney, we examined the role of phospholipase C-protein kinase C (PLC-PKC) pathway and of various eicosanoids in
this process, using microdissected rat proximal convoluted tubules. Dopamine (DA) and parathyroid hormone (either synthetic
PTH1-34 or PTH3-34) inhibited Na-K-ATPase activity in dose-dependent manner; this effect was reproduced by PKC530-558 fragment and blocked by the specific PKC inhibitor calphostin C, as well as by the PLC inhibitors neomycin and U-73122. Pump
inhibition by DA, PTH, or arachidonic acid, and by PKC activators phorbol dibutyrate (PDBu) or dioctanoyl glycerol (DiC8)
was abolished by ethoxyresorufin, an inhibitor of the cytochrome P450-dependent monooxygenase pathway, but was unaffected
by indomethacin or nordihydroguaiaretic acid, inhibitors of the cyclooxygenase and lipoxygenase pathways of the arachidonic
acid cascade, respectively. Furthermore, each of the three monooxygenase products tested (20-HETE, 12(R)-HETE, or 11,12-DHT)
caused a dose-dependent inhibition of the pump. The effect of DA, PTH, PDBu or DiC8, as well as that of 20-HETE was not altered
when sodium entry was blocked with the amiloride analog ethylisopropyl amiloride or increased with nystatin.
We conclude that short-term regulation of proximal tubule Na-K-ATPase activity by dopamine and parathyroid hormone occurs
via the PLC-PKC signal transduction pathway and is mediated by cytochrome P450-dependent monooxygenase products of arachidonic
acid metabolism, which may interact with the pump rather than alter sodium access to it.
Received: 7 January 1996/Revised: 24 April 1996 相似文献
7.
Linda Baumann Paul Baumann Nancy A. Moran Jonas Sandström Mylo Ly Thao 《Journal of molecular evolution》1999,48(1):77-85
The prokaryotic endosymbionts (Buchnera) of aphids are known to provision their hosts with amino acids that are limiting in the aphid diet. Buchnera from the aphids Schizaphis graminum and Diuraphis noxia have plasmids containing leuABCD, genes that encode enzymes of the leucine biosynthetic pathway, as well as genes encoding proteins probably involved in plasmid
replication (repA1 and repA2) and an open reading frame (ORF1) of unknown function. The newly reported plasmids closely resemble a plasmid previously described in Buchnera of the aphid Rhopalosiphum padi [Bracho AM, Martínez-Torres D, Moya A, Latorre A (1995) J Mol Evol 41:67–73]. Nucleotide sequence comparisons indicate conserved
regions which may correspond to an origin of replication and two promoters, as well as inverted repeats, one of which resembles
a rho-independent terminator. Phylogenetic analyses based on amino acid sequences of leu gene products and ORF1 resulted in trees identical to those obtained from endosymbiont chromosomal genes and the plasmid-borne
trpEG. These results are consistent with a single evolutionary origin of the leuABCD-containing plasmid in a common ancestor of Aphididae and the lack of plasmid exchange between endosymbionts of different
aphid species. Trees for ORF1 and repA (based on both nucleotides and amino acids) are used to examine the basis for leu plasmid differences between Buchnera of Thelaxes suberi and Aphididae. The most plausible explanation is that a single transfer of the leu genes to an ancestral replicon was followed by rearrangements. The related replicon in Buchnera of Pemphigidae, which lacks leuABCD, appears to represent the ancestral condition, implying that the plasmid location of the leu genes arose after the Pemphigidae diverged from other aphid families. This conclusion parallels previously published observations
for the unrelated trpEG plasmid, which is present in Aphididae and absent in Pemphigidae. Recruitment of amino acid biosynthetic genes to plasmids
has been ongoing in Buchnera lineages after the infection of aphid hosts.
Received: 9 March 1998 / Accepted: 18 May 1998. 相似文献
8.
Peek AS Gaut BS Feldman RA Barry JP Kochevar RE Lutz RA Vrijenhoek RC 《Journal of molecular evolution》2000,50(2):141-153
Nucleotide sequences at two mitochondrial genes from 57 individuals representing eight species of deep-sea clams (Vesicomyidae)
were examined for variation consistent with the neutral model of molecular evolution. One gene, cytochrome oxidase subunit
I (COI), deviated from the expectations of neutrality by containing an excess of intraspecific nonsynonymous polymorphism.
Additionally, one species, Calyptogena kilmeri, showed a significant excess of rare polymorphism specifically at the COI locus. In contrast, a second mitochondrial gene,
the large-subunit 16S ribosomal RNA gene (16S), showed little deviation from neutrality either between or within species.
Together, COI and 16S show no deviation from neutral expectations by the HKA test, produce congruent phylogenetic relationships
between species, and show correlated numbers of fixed differences between species and polymorphism within species. These patterns
of both neutral and nonneutral evolution within the mitochondrial genome are most consistent with a model where intraspecific
nonsynonymous polymorphism at COI is near neutrality. In addition to examining the forces of molecular evolution, we extend
hypotheses about interspecific relationships within this family for geographical locations previously unexamined by molecular
methods including habitats near the Middle Atlantic, the Aleutian Trench, and Costa Rica.
Received: 10 March 1999 / Accepted: 13 September 1999 相似文献
9.
Molecular Evolution of the Myeloperoxidase Family 总被引:4,自引:0,他引:4
Animal myeloperoxidase and its relatives constitute a diverse protein family, which includes myeloperoxidase, eosinophil
peroxidase, thyroid peroxidase, salivary peroxidase, lactoperoxidase, ovoperoxidase, peroxidasin, peroxinectin, cyclooxygenase,
and others. The members of this protein family share a catalytic domain of about 500 amino acid residues in length, although
some members have distinctive mosaic structures. To investigate the evolution of the protein family, we performed a comparative
analysis of its members, using the amino acid sequences and the coordinate data available today. The results obtained in this
study are as follows: (1) 60 amino acid sequences belonging to this family were collected by database searching. We found
a new member of the myeloperoxidase family derived from a bacterium. This is the first report of a bacterial member of this
family. (2) An unrooted phylogenetic tree of the family was constructed according to the alignment. Considering the branching
pattern in the obtained phylogenetic tree, together with the mosaic features in the primary structures, 60 members of the
myeloperoxidase family were classified into 16 subfamilies. (3) We found two molecular features that distinguish cyclooxygenase
from the other members of the protein family. (4) Several structurally deviated segments were identified by a structural comparison
between cyclooxygenase and myeloperoxidase. Some of the segments seemed to be associated with the functional and/or structural
differences between the enzymes.
Received: 25 January 2000 / Accepted: 19 July 2000 相似文献
10.
11.
Syvanen M 《Journal of molecular evolution》2002,54(2):258-266
The deduced amino acid sequences from 1200 Haemophilus influenzae genes was compared to a data set that contained the orfs from yeast, two different Archaea and the Gram+ and Gram− bacteria,
Bacillus subtilis and Escherichia coli. The results of the comparison yielded a 26 orthologous gene set that had at least one representative from each of the four
groups. A four taxa phylogenetic relationship for these 26 genes was determined. The statistical significance of each minimal
tree was tested against the two alternative four taxa trees. The result was that four genes significantly supported the (Archaea,
Eukaryota) (Gram+, Gram−) topology, two genes supported the one where Gram− and Eukaryota form a clade, and one gene supported
the tree where Gram+ and Eukaryota define one clade. The remaining genes do not uniquely support any phylogeny, thereby collapsing
the two central nodes into a single node. These are referred to as star phylogenies.
I offer a new suggestion for the mechanism that gave rise to the star phylogenies. Namely, these are genes that are younger
than the underlying lineages that currently harbor them. This hypothesis is examined with two proteins that display the star
phylogeny; namely onithine transcarbamylase and tryptophan synthetase. It is shown, using the distance matrix rate test, that
the rate of evolution of these two proteins is comparable to a control gene when rates are determined by comparing closely
related species. This implies that the genes under comparison experience comparable functional constraint. However, when the
genes from remotely related species are compared, a plateau is encountered. Since we see no unusual levels of functional constraint
this plateau cannot be attributed to the divergence of the protein having reached saturation. The simplest explanation is
that the genes displaying the star phylogenies were introduced after Archaea, Eukaryota, and Bacteria had diverged from one
another. They presumably spread through life by horizontal gene transfer.
Received: 12 July 2001 / Accepted: 27 July 2001 相似文献
12.
Peter E.M. Gibbs Werner F. Witke Achilles Dugaiczyk 《Journal of molecular evolution》1998,46(5):552-561
The serum albumin gene family is composed of four members that have arisen by a series of duplications from a common ancestor.
From sequence differences between members of the gene family, we infer that a gene duplication some 580 Myr ago gave rise
to the vitamin D–binding protein (DBP) gene and a second lineage, which reduplicated about 295 Myr ago to give the albumin
(ALB) gene and a common precursor to α-fetoprotein (AFP) and α-albumin (ALF). This precursor itself duplicated about 250 Myr
ago, giving rise to the youngest family members, AFP and ALF. It should be possible to correlate these dates with the phylogenetic
distribution of members of the gene family among different species. All four genes are found in mammals, but AFP and ALF are
not found in amphibia, which diverged from reptiles about 360 Myr ago, before the divergence of the AFP-ALF progenitor from
albumin.
Although individual family members display an approximate clock-like evolution, there are significant deviations—the rates
of divergence for AFP differ by a factor of 7, the rates for ALB differ by a factor of 2.1. Since the progenitor of this gene
family itself arose by triplication of a smaller gene, the rates of evolution of individual domains were also calculated and
were shown to vary within and between family members. The great variation in the rates of the molecular clock raises questions
concerning whether it can be used to infer evolutionary time from contemporary sequence differences.
Received: 28 February 1995 / Accepted: 6 October 1997 相似文献
13.
《Molecular & cellular proteomics : MCP》2019,18(12):2478-2491
Highlights
- •Deep learning-based hybrid de novo sequencing with database search strategy.
- •Accurate identifications via ability to revise confidence scores and amino acids.
- •Discovery of >10,000 potential new HLA antigens and human phosphopeptides.
- •A dataset of >26 million annotated HCD spectra from Q Exactive instruments.
14.
Five cDNAs (pDidact2–pDidact6), representing different actin genes, were isolated from a Diphyllobothrium dendriticum cDNA library, and the DNA as well as the putative amino acid sequences were determined. The corresponding Didact2 and Didact4 genes code for peptides 376 amino acids long, with molecular weights 41,772 and 41,744 Da, respectively, while the deduced
Didact3 protein is 377 amino acids long and weighs 41,912 Da. The pDidact5 and -6 cDNAs lack nucleotides corresponding to three to six amino acids at the amino-terminus. Two of the five cDNAs contain the
conventional AATAAA as the putative polyadenylation signal, one has the common variant ATTAAA, whereas the hexanucleotide
AATAGA is found 15 and 18 nucleotides, respectively, upstream of the poly(A) site in two of the cDNAs. Phylogenetic studies
including 102 actin protein sequences revealed that there are at least four different types of cestode actins. In this study
three of these types were found to be expressed in the adult D. dendriticum tapeworm. Structurally the cestode actin groupings differ from each other to an extent seen only among the metazoan actins
between the vertebrate muscle and cytoplasmic isoforms. In the phylogenetic trees constructed, cestode actins were seen to
map to two different regions, one on the border of the metazoan actins and the other within this group. It is, however, difficult
to say whether the cestode actins branched off early in the metazoan evolution or if this position in the phylogenetic tree
only reflects upon differences in evolutionary rate.
Received: 19 June 1996 / Accepted: 20 August 1996 相似文献
15.
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
16.
Summary
Bumetanide-sensitive Na-K-Cl cotransporters and thiazide-sensitive Na-Cl cotransporters comprise a family of integral membrane
transport proteins, the Na-K-Cl cotransporter (NKCC) family. Each of the members of this family is over 1,000 amino acids
in length. We have multiply aligned the ten currently sequenced members of this family from human, rabbit, rodent, shark,
flounder, moth, worm and yeast sources. Phylogenetic analyses suggest the presence of at least six isoforms of these full
length proteins in eukaryotes. Average hydropathy and average similarity plots have been derived revealing that each of these
proteins possesses a central, well conserved, hydrophobic domain of almost invariant length, possibly consisting of twelve
transmembrane α-helical spanners, an N-terminal, poorly conserved, hydrophilic domain of variable length, and a C-terminal,
moderately conserved, hydrophilic domain of moderately constant length. A functionally uncharacterized homologue of this family
occurs in the cyanobacterium Synechococcus sp. Limited sequence similarity of these proteins with members of a family of basic amino acid transporters suggests that the
NKCC family may be distantly related to the previously characterized, ubiquitous, amino acid-polyamine-choline (APC) family
of facilitators. These observations suggest that the NKCC family is an old family that has its roots in the prokaryotic kingdom.
Received: 27 July 1995/Revised: 8 November 1995 相似文献
17.
To investigate the causes and functional significance of rapid sex-determining protein evolution we compared three Caenorhabditis elegans genes encoding members of the protein phosphatase 2C (PP2C) family with their orthologs from another Caenorhabditis species (strain CB5161). One of the genes encodes FEM-2, a sex-determining protein, while the others have no known sex-determining
role. FEM-2's PP2C domain was found to be more diverged than the other PP2C domains, supporting the notion that sex-determining
proteins are subjected to selective pressures that allow for or cause rapid divergence. Comparison of the positions of amino
acid substitutions in FEM-2 with a solved three-dimensional structure suggests that the catalytic face of the protein is highly
conserved among C. elegans, CB5161, and another closely related species C. briggsae. However, the non-conserved regions of FEM-2 cannot be said to lack functional importance, since fem-2 transgenes from the other species were unable to rescue the germ-line defect caused by a C. elegans fem-2 mutation. To test whether fem-2 functions as a sex-determining gene in the other Caenorhabditis species we used RNA-mediated interference (RNAi). fem-2 (RNAi) in C. elegans and C. briggsae caused germ-line feminization, but had no noticeable effect in CB5161. Thus the function of fem-2 in CB5161 remains uncertain.
Received: 11 April 2001 / Accepted: 6 August 2001 相似文献
18.
Many of the biosynthetic pathways, especially those leading to the coenzymes, must have originated very early, perhaps before
enzymes were available to catalyze their synthesis. While a number of enzymatic reactions in metabolism are known to proceed
nonenzymatically, there are no examples of entire metabolic sequences that can be achieved in this manner. The most primitive
pathway for nicotinic acid biosynthesis is the reaction of aspartic acid with dihydroxyacetone phosphate. We report here that
nicotinic acid (NAc) and its metabolic precursor, quinolinic acid (QA), are produced in yields as high as 7% in a six-step
nonenzymatic sequence from aspartic acid and dihydroxyacetone phosphate (DHAP). The biosynthesis of ribose phosphate could
have produced DHAP and other three carbon compounds. Aspartic acid could have been available from prebiotic synthesis or from
the ribozyme synthesis of pyrimidines. These results suggest that NAD could have originated in the RNA world and that the
nonenzymatic biosynthesis of the cofactor nicotinamide could have been an inevitable consequence of life based on carbohydrates
and amino acids. The enzymes of the modern pathway were later added in any order.
Received: 22 May 2000 / Accepted: 7 August 2000 相似文献
19.
Homologues of the Na+/glucose cotransporter, the SGLT family, include sequences of mammalian, eubacterial, yeast, insect and nematode origin. The
cotransported substrates are sugars, inositol, proline, pantothenate, iodide, urea and undetermined solutes. It is reasonable
to expect that the SGLT family members share a similar or identical topology of membrane spanning elements, by virtue of their
common ancestry and similar coupling of solute transport to downhill sodium flux. Here we examine their membrane topologies
as deduced from diverse analyses of their primary sequences, and from their sequence correlations with the experimentally
determined topology of the human Na+/glucose cotransporter SGLT1. Our analyses indicate that all family members share a common core of 13 transmembrane helices,
but that some, like SGLT1 itself, have one additional span appended to the C-terminus, and still others, two. One bacterial
member incorporates an additional span at the N-terminus. Sequence comparisons indicative of common ancestry of the SGLT and
the [Na++ Cl−] transporter families are introduced, and evaluated in light of their topologies. New evidence concerning the previously
asserted common ancestry of SGLT1 and an N-acetylglucosamine permease of the bacterial phosphotransferase system is considered.
Finally, we analyze observations which lead us to conjecture that the experimental strategy most commonly employed to reveal
the topology of bacterial transporters (i.e., the fusion of reporter enzymes such as phoA alkaline phosphatase, beta-lactamase
or beta-galactosidase, to progressively C-truncated fragments of the transporter) has often instead so perturbed local topology
as to have entirely missed pairs of adjacent membrane spans.
Received: 18 May 1996 相似文献
20.
Philippe Castagnone-Sereno Hélène Leroy Jean-Philippe Semblat Frédéric Leroy Pierre Abad Carolien Zijlstra 《Journal of molecular evolution》1998,46(2):225-233
An AluI satellite DNA family has been isolated in the genome of the root-knot nematode Meloidogyne chitwoodi. This repeated sequence was shown to be present at approximately 11,400 copies per haploid genome, and represents about 3.5%
of the total genomic DNA. Nineteen monomers were cloned and sequenced. Their length ranged from 142 to 180 bp, and their A
+ T content was high (from 65.7 to 79.1%), with frequent runs of As and Ts. An unexpected heterogeneity in primary structure
was observed between monomers, and multiple alignment analysis showed that the 19 repeats could be unambiguously clustered
in six subfamilies. A consensus sequence has been deduced for each subfamily, within which the number of positions conserved
is very high, ranging from 86.7% to 98.6%. Even though blocks of conserved regions could be observed, multiple alignment of
the six consensus sequences did not enable the establishment of a general unambiguous consensus sequence. Screening of the
six consensus sequences for evidence of internal repeated subunits revealed a 6-bp motif (AAATTT), present in both direct
and inverted orientation. This motif was found up to nine times in the consensus sequences, also with the occurrence of degenerated
subrepeats. Along with the meiotic parthenogenetic mode of reproduction of this nematode, such structural features may argue
for the evolution of this satellite DNA family either (1) from a common ancestral sequence by amplification followed by mechanisms
of sequence divergence, or (2) through independent mutations of the ancestral sequence in isolated amphimictic nematode populations
and subsequent hybridization events. Overall, our results suggest the ancient origin of this satellite DNA family, and may
reflect for M. chitwoodi a phylogenetic position close to the ancestral amphimictic forms of root-knot nematodes.
Received: 23 April 1997 / Accepted: 9 July 1997 相似文献