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1.
The pairs of nitrogen fixation genes nifDK and nifEN encode for the α and β subunits of nitrogenase and for the two subunits of the NifNE protein complex, involved in the biosynthesis
of the FeMo cofactor, respectively. Comparative analysis of the amino acid sequences of the four NifD, NifK, NifE, and NifN
in several archaeal and bacterial diazotrophs showed extensive sequence similarity between them, suggesting that their encoding
genes constitute a novel paralogous gene family. We propose a two-step model to reconstruct the possible evolutionary history
of the four genes. Accordingly, an ancestor gene gave rise, by an in-tandem paralogous duplication event followed by divergence,
to an ancestral bicistronic operon; the latter, in turn, underwent a paralogous operon duplication event followed by evolutionary
divergence leading to the ancestors of the present-day nifDK and nifEN operons. Both these paralogous duplication events very likely predated the appearance of the last universal common ancestor.
The possible role of the ancestral gene and operon in nitrogen fixation is also discussed.
Received: 21 June 1999 / Accepted: 1 March 2000 相似文献
2.
Evolution of Chitin-Binding Proteins in Invertebrates 总被引:11,自引:0,他引:11
Analysis of a group of invertebrate proteins, including chitinases and peritrophic matrix proteins, reveals the presence
of chitin-binding domains that share significant amino acid sequence similarity. The data suggest that these domains evolved
from a common ancestor which may be a protein containing a single chitin-binding domain. The duplication and transposition
of this chitin-binding domain may have contributed to the functional diversification of chitin-binding proteins. Sequence
comparisons indicated that invertebrate and plant chitin binding domains do not share significant amino acid sequence similarity,
suggesting that they are not coancestral. However, both the invertebrate and the plant chitin-binding domains are cysteine-rich
and have several highly conserved aromatic residues. In plants, cysteines have been elucidated in maintaining protein folding
and aromatic amino acids in interacting with saccharides [Wright HT, Sanddrasegaram G, Wright CS (1991) J Mol Evol 33:283–294].
It is likely that these residues perform similar functions in invertebrates. We propose that the invertebrate and the plant
chitin-binding domains share similar mechanisms for folding and saccharide binding and that they evolved by convergent evolution.
Furthermore, we propose that the disulfide bonds and aromatic residues are hallmarks for saccharide-binding proteins.
Received: 2 March 1998 / Accepted: 17 July 1998 相似文献
3.
The ribosomal protection proteins (RPPs) mediate the resistance to tetracycline (TC) in Gram-positive and Gram-negative bacteria.
The RPPs display sequence similarity to translation elongation factors, EF-G/EF-2 and EF-Tu/EF-1α. To determine the evolutionary
origin of the RPPs, we constructed a composite phylogenetic tree of the RPPs, EF-G/EF-2 and EF-Tu/EF-1α. This tree includes
two universal trees for the EF-G/EF-2 and EF-Tu/EF-1α, which form clusters corresponding to the respective two groups of proteins
from three superkingdoms. The cluster of RPPs was placed at a point between the EF-G/EF-2 and EF-Tu/EF-1α clusters. The branch
length (substitutions/site) between the node for the RPP cluster and the primary divergence of the RPPs was statistically
shorter than that between the node for this cluster and the primary divergence in the EF-G/EF-2 cluster. This indicates that
the RPPs derived through duplication and divergence of the ancient GTPase before the divergence of the three superkingdoms.
Furthermore, this suggests the RPPs’ extant function occurred before the streptomycetes that include the TC-producing strains.
Therefore, the RPPs evolved independent of the presence of TCs and serve a function other than antibiotic resistance. The
RPPs may provide ribosomal protection against other chemical substances in the environment.
Reviewing
Editor: Dr. Margaret Riley
Takeshi Kobayashi, Lisa Nonaka have contributed significantly to the research and preparation of this article. 相似文献
4.
Piero Cammarano Roberta Creti Anna M. Sanangelantoni Peter Palm 《Journal of molecular evolution》1999,49(4):524-537
A global alignment of EF-G(2) sequences was corrected by reference to protein structure. The selection of characters eligible
for construction of phylogenetic trees was optimized by searching for regions arising from the artifactual matching of sequence
segments unique to different phylogenetic domains. The spurious matchings were identified by comparing all sections of the
global alignment with a comprehensive inventory of significant binary alignments obtained by BLAST probing of the DNA and
protein databases with representative EF-G(2) sequences. In three discrete alignment blocks (one in domain II and two in domain
IV), the alignment of the bacterial sequences with those of Archaea–Eucarya was not retrieved by database probing with EF-G(2)
sequences, and no EF-G homologue of the EF-2 sequence segments was detected by using partial EF-G(2) sequences as probes in
BLAST/FASTA searches. The two domain IV regions (one of which comprises the ADP-ribosylatable site of EF-2) are almost certainly
due to the artifactual alignment of insertion segments that are unique to Bacteria and to Archaea–Eucarya. Phylogenetic trees
have been constructed from the global alignment after deselecting positions encompassing the unretrieved, spuriously aligned
regions, as well as positions arising from misalignment of the G′ and G″ subdomain insertion segments flanking the ``fifth'
consensus motif of the G domain (?varsson, 1995). The results show inconsistencies between trees inferred by alternative methods
and alternative (DNA and protein) data sets with regard to Archaea being a monophyletic or paraphyletic grouping. Both maximum-likelihood
and maximum-parsimony methods do not allow discrimination (by log-likelihood difference and difference in number of inferred
substitutions) between the conflicting (monophyletic vs. paraphyletic Archaea) topologies. No specific EF-2 insertions (or
terminal accretions) supporting a crenarchaeal–eucaryal clade are detectable in the new EF-G(2) sequence alignment. 相似文献
5.
Elongation factor (EF) Tu alternates between two interaction partners, EF-Ts and the ribosome, during its functional cycle.
On the ribosome, the interaction involves, among others, ribosomal protein L7/12. Here we compare EF-Ts and L7/12 with respect
to the conservation of sequence and structure. There is significant conservation of functionally important residues in the
N-terminal domain of EF-Ts and in the C-terminal domain of L7/12. The structure alignment based on the crystal structures
of the two domains suggests a high degree of similarity between the αA–βD–αB motif in L7/12 and the h1–turn–h2 motif in EF-Ts
which defines a common structural motif. The motif is remarkably similar with respect to fold, bulkiness, and charge distribution
of the solution surface, suggesting that it has a common function in binding EF-Tu.
Received: 12 June 2000 / Accepted: 10 October 2000 相似文献
6.
The Root of the Universal Tree of Life Inferred from Anciently Duplicated Genes Encoding Components of the Protein-Targeting Machinery 总被引:5,自引:0,他引:5
The key protein of the signal recognition particle (termed SRP54 for Eucarya and Ffh for Bacteria) and the protein (termed
SRα for Eucarya and Ftsy for bacteria) involved in the recognition and binding of the ribosome SRP nascent polypeptide complex
are the products of an ancient gene duplication that appears to predate the divergence of all extant taxa. The paralogy of
the genes encoding the two proteins (both of which are GTP triphosphatases) is argued by obvious sequence similarities between
the N-terminal half of SRP54(Ffh) and the C-terminal half of SRα(Ftsy). This enables a universal phylogeny based on either
protein to be rooted using the second protein as an outgroup. Phylogenetic trees inferred by various methods from an alignment
(220 amino acid positions) of the shared SRP54(Ffh) and SRα(Ftsy) regions generate two reciprocally rooted universal trees
corresponding to the two genes. The root of both trees is firmly positioned between Bacteria and Archaea/Eucarya, thus providing
strong support for the notion (Iwabe et al. 1989; Gogarten et al. 1989) that the first bifurcation in the tree of life separated
the lineage leading to Bacteria from a common ancestor to Archaea and Eucarya. None of the gene trees inferred from the two
paralogues support a paraphyletic Archaea with the crenarchaeota as a sister group to Eucarya.
Received: 19 March 1998 / Accepted: 5 June 1998 相似文献
7.
Charles Robin Robyn J. Russell Kerrie M. Medveczky John G. Oakeshott 《Journal of molecular evolution》1996,43(3):241-252
The α-esterase cluster of D. melanogaster contains 11 esterase genes dispersed over 60 kb. Embedded in the cluster are two unrelated open reading frames that have
sequence similarity with genes encoding ubiquitin-conjugating enzyme and tropomyosin. The esterase amino acid sequences show
37–66% identity with one another and all but one have all the motifs characteristic of functional members of the carboxyl/cholinesterase
multigene family. The exception has several frameshift mutations and appears to be a pseudogene. Patterns of amino acid differences
among cluster members in relation to generic models of carboxyl/cholinesterase protein structure are broadly similar to those
among other carboxyl/cholinesterases sequenced to date. However the α-esterases differ from most other members of the family
in: their lack of a signal peptide; the lack of conservation in cysteines involved in disulfide bridges; and in four indels,
two of which occur in or adjacent to regions that align with proposed substrate-binding sites of other carboxyl/cholinesterases.
Phylogenetic analyses clearly identify three simple gene duplication events within the cluster. The most recent event involved
the pseudogene which is located in an intron of another esterase gene. However, relative rate tests suggest that the pseudogene
remained functional after the duplication event and has become inactive relatively recently. The distribution of indels also
suggests a deeper node in the gene phylogeny that separates six genes at the two ends of the cluster from a block of five
in the middle.
Received: 18 January 1996 / Accepted: 12 March 1996 相似文献
8.
Eukaryotic vesicular transport requires the recognition of membranes through specific protein complexes. The heterotetrameric
adaptor protein complexes 1, 2, and 3 (AP1/2/3) are composed of two large, one small, and one medium adaptin subunit. We isolated
and characterized the cDNA for Arabidopsisγ-adaptin and performed a phylogenetic analysis of all adaptin subunits (proteins) in the context of all known homologous
proteins. This analysis revealed (i) that the large subunits of AP1/2/3 are homologous and (ii) two subunits of the heptameric
coatomer I (COPI) complex belong to this gene family. In addition, all small subunits and the aminoterminal domain of the
medium subunits of the heterotetramers are homologous to each other; this also holds for two corresponding subunits of the
COPI complex. AP1/2/3 and a substructure (heterotetrameric, F-COPI subcomplex) of the heptameric COPI had a common ancestral
complex (called pre-F-COPI). Since all large and all small/medium subunits share sequence similarity, the ancestor of this
complex is inferred to have been a heterodimer composed of one large and one small subunit. The situation encountered today
is the result of successive rounds of coordinated gene duplications of both the large and the small/medium subunits, with
F-COPI being the first that separated from the ancestral pre-F-COPI.
Received: 1 October 1998 / Accepted: 4 January 1999 相似文献
9.
The AAA proteins (ATPases Associated with a variety of cellular Activities) are found in eubacterial, archaebacterial, and eukaryotic species and participate in a large number of cellular
processes, including protein degradation, vesicle fusion, cell cycle control, and cellular secretory processes. The AAA proteins
are characterized by the presence of a 230 to 250-amino acid ATPase domain referred to as the Conserved ATPase Domain or CAD. Phylogenetic analysis of 133 CAD sequences from 38 species reveal that AAA CADs are organized into discrete
groups that are related not only in structure but in cellular function. Evolutionary analyses also indicate that the CAD was
present in the last common ancestor of eubacteria, archaebacteria, and eukaryotes. The eubacterial CADs are found in metalloproteases,
while CAD-containing proteins in the archaebacterial and eukaryotic lineages appear to have diversified by a series of gene
duplication events that lead to the establishment of different functional AAA proteins, including proteasomal regulatory,
NSF/Sec, and Pas proteins. The phylogeny of the CADs provides the basis for establishing the patterns of evolutionary change
that characterize the AAA proteins.
Received: 28 January 1997 / Accepted: 8 May 1997 相似文献
10.
In this paper we analyzed 49 lactate dehydrogenase (LDH) sequences, mostly from vertebrates. The amino acid sequence differences
were found to be larger for a human–killifish pair than a human–lamprey pair. This indicates that some protein sequence convergence
may occur and reduce the sequence differences in distantly related species. We also examined transitions and transversions
separately for several species pairs and found that the transitions tend to be saturated in the distantly related species
pair, while transversions are increasing. We conclude that transversions maintain a conservative rate through the evolutionary
time. Kimura's two-parameter model for multiple-hit correction on transversions only was used to derive a distance measure
and then construct a neighbor-joining (NJ) tree. Three findings were revealed from the NJ tree: (i) the branching order of
the tree is consistent with the common branch pattern of major vertebrates; (ii) Ldh-A and Ldh-B genes were duplicated near the origin of vertebrates; and (iii) Ldh-C and Ldh-A in mammals were produced by an independent gene duplication in early mammalian history. Furthermore, a relative rate test
showed that mammalian Ldh-C evolved more rapidly than mammalian Ldh-A. Under a two-rate model, this duplication event was calibrated to be approximately 247 million years ago (mya), dating back
to the Triassic period. Other gene duplication events were also discovered in Xenopus, the first duplication occurring approximately 60–70 mya in both Ldh-A and Ldh-B, followed by another recent gene duplication event, approximately 20 mya, in Ldh-B.
Received: 5 October 2001 / Accepted: 24 October 2001 相似文献
11.
Primary Structure and Phylogenetic Relationships of a Malate Dehydrogenase Gene from Giardia lamblia
The lactate and malate dehydrogenases comprise a complex protein superfamily with multiple enzyme homologues found in eubacteria,
archaebacteria, and eukaryotes. In this study we describe the sequence and phylogenetic relationships of a malate dehydrogenase
(MDH) gene from the amitochondriate diplomonad protist, Giardia lamblia. Parsimony, distance, and maximum-likelihood analyses of the MDH protein family solidly position G. lamblia MDH within a eukaryote cytosolic MDH clade, to the exclusion of chloroplast, mitochondrial, and peroxisomal homologues. Furthermore,
G. lamblia MDH is specifically related to a homologue from Trichomonas vaginalis. This MDH topology, together with published phylogenetic analyses of β-tubulin, chaperonin 60, valyl-tRNA synthetase, and
EF-1α, suggests a sister-group relationship between diplomonads and parabasalids. Since these amitochondriate lineages contain
genes encoding proteins which are characteristic of mitochondria and α-proteobacteria, their shared ancestry suggests that
mitochondrial properties were lost in the common ancestor of both groups.
Received: 14 September 1998 / Accepted: 29 December 1998 相似文献
12.
Patrick J. Keeling Naomi M. Fast Geoff I. McFadden 《Journal of molecular evolution》1998,47(6):649-655
Eubacterial and eukaryotic translation initiation systems have very little in common, and therefore the evolutionary events
that gave rise to these two disparate systems are difficult to ascertain. One common feature is the presence of initiation,
elongation, and release factors belonging to a large GTPase superfamily. One of these initiation factors, the γ subunit of
initiation factor 2 (eIF-2γ), is found only in eukaryotes and archaebacteria. We have sequenced eIF-2γ gene fragments from
representative diplomonads, parabasalia, and microsporidia and used these new sequences together with new archaebacterial
homologues to examine the phylogenetic position of eIF-2γ within the GTPase superfamily. The archaebacterial and eukaryotic
eIF-2γ proteins are found to be very closely related, and are in turn related to SELB, the selenocysteine-specific elongation
factor from eubacteria. The overall topology of the GTPase tree further suggests that the eIF-2γ/SELB group may represent
an ancient subfamily of GTPases that diverged prior to the last common ancestor of extant life.
Received: 2 January 1998 / Accepted: 1 June 1998 相似文献
13.
Sequences from the tuf gene coding for the elongation factor EF-Tu were amplified and sequenced from the genomic DNA of Pirellula marina and Isosphaera pallida, two species of bacteria within the order Planctomycetales. A near-complete (1140-bp) sequence was obtained from Pi. marina and a partial (759-bp) sequence was obtained for I. pallida. Alignment of the deduced Pi. marina EF-Tu amino acid sequence against reference sequences demonstrated the presence of a unique 11-amino acid sequence motif
not present in any other division of the domain Bacteria. Pi. marina shared the highest percentage amino acid sequence identity with I. pallida but showed only a low percentage identity with other members of the domain Bacteria. This is consistent with the concept
of the planctomycetes as a unique division of the Bacteria. Neither primary sequence comparison of EF-Tu nor phylogenetic
analysis supports any close relationship between planctomycetes and the chlamydiae, which has previously been postulated on
the basis of 16S rRNA. Phylogenetic analysis of aligned EF-Tu amino acid sequences performed using distance, maximum-parsimony,
and maximum-likelihood approaches yielded contradictory results with respect to the position of planctomycetes relative to
other bacteria. It is hypothesized that long-branch attraction effects due to unequal evolutionary rates and mutational saturation
effects may account for some of the contradictions.
Received: 21 August 2000 / Accepted: 8 January 2001 相似文献
14.
One of the most remarkable biochemical differences between the members of two domains Archaea and Bacteria is the stereochemistry
of the glycerophosphate backbone of phospholipids, which are exclusively opposite. The enzyme responsible to the formation
of Archaea-specific glycerophosphate was found to be NAD(P)-linked sn-glycerol-1-phosphate (G-1-P) dehydrogenase and it was first purified from Methanobacterium thermoautotrophicum cells and its gene was cloned. This structure gene named egsA (enantiomeric glycerophosphate synthase) consisted of 1,041 bp and coded the enzyme with 347 amino acid residues. The amino
acid sequence deduced from the base sequence of the cloned gene (egsA) did not share any sequence similarity except for NAD-binding region with that of NAD(P)-linked sn-glycerol-3-phosphate (G-3-P) dehydrogenase of Escherichia coli which catalyzes the formation of G-3-P backbone of bacterial phospholipids, while the deduced protein sequence of the enzyme
revealed some similarity with bacterial glycerol dehydrogenases. Because G-1-P dehydrogenase and G-3-P dehydrogenase would
originate from different ancestor enzymes and it would be almost impossible to interchange stereospecificity of the enzymes,
it seems likely that the stereostructure of membrane phospholipids of a cell must be maintained from the time of birth of
the first cell. We propose here the hypothesis that Archaea and Bacteria were differentiated by the occurrence of cells enclosed
by membranes of phospholipids with G-1-P and G-3-P as a backbone, respectively.
Received: 24 March 1997 / Accepted: 21 May 1997 相似文献
15.
16.
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
17.
Bujnicki JM 《Journal of molecular evolution》2000,50(1):39-44
To date all attempts to derive a phyletic relationship among restriction endonucleases (ENases) from multiple sequence alignments
have been limited by extreme divergence of these enzymes. Based on the approach of Johnson et al. (1990), I report for the
first time the evolutionary tree of the ENase-like protein superfamily inferred from quantitative comparison of atomic coordinates
of structurally characterized enzymes. The results presented are in harmony with previous comparisons obtained by crystallographic
analyses. It is shown that λ-exonuclease initially diverged from the common ancestor and then two ``endonucleolytic' families
branched out, separating ``blunt end cutters' from ``5′ four-base overhang cutters.' These data may contribute to a better
understanding of ENases and encourage the use of structure-based methods for inference of phylogenetic relationship among
extremely divergent proteins. In addition, the comparison of three-dimensional structures of ENase-like domains provides a
platform for further clustering analyses of sequence similarities among different branches of this large protein family, rational
choice of homology modeling templates, and targets for protein engineering.
Received: 14 June 1999 / Accepted: 11 August 1999 相似文献
18.
19.
The available amino acid sequences of the α-amylase family (glycosyl hydrolase family 13) were searched to identify their
domain B, a distinct domain that protrudes from the regular catalytic (β/α)8-barrel between the strand β3 and the helix α3. The isolated domain B sequences were inspected visually and also analyzed
by Hydrophobic Cluster Analysis (HCA) to find common features. Sequence analyses and inspection of the few available three-dimensional
structures suggest that the secondary structure of domain B varies with the enzyme specificity. Domain B in these different
forms, however, may still have evolved from a common ancestor. The largest number of different specificities was found in
the group with structural similarity to domain B from Bacillus cereus oligo-1,6-glucosidase that contains an α-helix succeeded by a three-stranded antiparallel β-sheet. These enzymes are α-glucosidase,
cyclomaltodextrinase, dextran glucosidase, trehalose-6-phosphate hydrolase, neopullulanase, and a few α-amylases. Domain B
of this type was observed also in some mammalian proteins involved in the transport of amino acids. These proteins show remarkable
similarity with (β/α)8-barrel elements throughout the entire sequence of enzymes from the oligo-1,6-glucosidase group. The transport proteins, in
turn, resemble the animal 4F2 heavy-chain cell surface antigens, for which the sequences either lack domain B or contain only
parts thereof. The similarities are compiled to indicate a possible route of domain evolution in the α-amylase family.
Received: 4 December 1996 / Accepted: 13 March 1997 相似文献
20.
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