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1.
Christiane Elie Marie- France Baucher Christian Fondrat Patrick Forterre 《Journal of molecular evolution》1997,45(1):107-114
We have isolated a new gene encoding a putative 103-kDa protein from the hyperthermophilic archaeon Sulfolobus acidocaldarius. Analysis of the deduced amino-acid sequence shows an extended central domain, predicted to form coiled-coil structures, and
two terminal domains that display purine NTPase motifs. These features are reminiscent of mechanochemical motor proteins which
use the energy of ATP hydrolysis to move specific cellular components. Comparative analysis of the amino-acid sequence of
the terminal domains and predicted structural organization of this putative purine NTPase show that it is related both to
eucaryal proteins from the ``SMC family' involved in the condensation of chromosomes and to several bacterial and eucaryal
proteins involved in DNA recombination/repair. Further analyses revealed that these proteins are all members of the so called
``UvrA-related NTP-binding proteins superfamily' and form a large subgroup of motor-like NTPases involved in different DNA
processing mechanisms. The presence of such protein in Archaea, Bacteria, and Eucarya suggests an early origin of DNA-motor
proteins that could have emerged and diversified by domain shuffling.
Received: 29 June 1996 / Accepted: 28 February 1997 相似文献
2.
F Lindberg J M Tennent S J Hultgren B Lund S Normark 《Journal of bacteriology》1989,171(11):6052-6058
The product of the papD gene of uropathogenic Escherichia coli is required for the biogenesis of digalactoside-binding P pili. Mutations within papD result in complete degradation of the major pilus subunit, PapA, and of the pilinlike proteins PapE and PapF and also cause partial breakdown of the PapG adhesin. The papD gene was sequenced, and the gene product was purified from the periplasm. The deduced amino acid sequence and the N-terminal sequence obtained from the purified protein revealed that PapD is a basic and hydrophilic peripheral protein. A periplasmic complex between PapD and PapE was purified from cells that overproduced and accumulated these proteins in the periplasm. Antibodies raised against this complex reacted with purified wild-type P pili but not with pili purified from a papE mutant. In contrast, anti-PapD serum did not react with purified pili or with the culture fluid of piliated cells. However, this serum was able to specifically precipitate the PapE protein from periplasmic extracts, confirming that PapD and PapE were associated as a complex. It is suggested that PapD functions in P-pilus biogenesis as a periplasmic transport protein. Probably PapD forms complexes with pilus subunits at the outer surface of the inner membrane and transports them in a stable configuration across the periplasmic space before delivering them to the site(s) of pilus polymerization. 相似文献
3.
Gene structure of a chlorophyll a/c-binding protein from a brown alga: Presence of an intron and phylogenetic implications 总被引:5,自引:0,他引:5
Lise Caron Dominique Douady Michelle Quinet-Szely Susan de Goër Claire Berkaloff 《Journal of molecular evolution》1996,43(3):270-280
A Laminaria saccharina genomic library in the phage EMBL 4 was used to isolate and sequence a full-length gene encoding a fucoxanthin-chlorophyll
a/c-binding protein. Contrary to diatom homologues, the coding sequence is interrupted by an intron of about 900 bp which
is located in the middle of the transit peptide. The deduced amino acid sequence of the mature protein is very similar to
those of related proteins from Macrocystis pyrifera (Laminariales) and, to a lesser extent, to those from diatoms and Chrysophyceae. Seven of the eight putative chlorophyll-binding
amino acids determined in green plants are also present. Alignments of different sequences related to the light-harvesting
proteins (LHC) demonstrate a structural similarity among the three transmembrane helices and suggest a unique ancestral helix
preceded by two β-turns. The β-turns are conserved in front of the second helices of the chlorophyll a/c proteins more so
than in chlorophyll a/b proteins. Phylogenetic trees generated from sequence data indicate that fucoxanthin-chlorophyll-binding
proteins diverged prior to the separation of photosystem I and photosystem II LHC genes of green plants. Among the fucoxanthin-containing
algae, LHC I or II families could not be distinguished at this time.
Received: 14 February 1996 / Accepted: 4 April 1996 相似文献
4.
Interactive surface in the PapD chaperone cleft is conserved in pilus chaperone superfamily and essential in subunit recognition and assembly. 总被引:9,自引:0,他引:9 下载免费PDF全文
The assembly of adhesive pili in Gram-negative bacteria is modulated by specialized periplasmic chaperone systems. PapD is the prototype member of the superfamily of periplasmic pilus chaperones. Previously, the alignment of chaperone sequences superimposed on the three dimensional structure of PapD revealed the presence of invariant, conserved and variable amino acids. Representative residues that protruded into the PapD cleft were targeted for site directed mutagenesis to investigate the pilus protein binding site of the chaperone. The ability of PapD to bind to fiber-forming pilus subunit proteins to prevent their participation in misassembly interactions depended on the invariant, solvent-exposed arginine-8 (R8) cleft residue. This residue was also essential for the interaction between PapD and a minor pilus adaptor protein. A mutation in the conserved methionine-172 (M172) cleft residue abolished PapD function when this mutant protein was expressed below a critical threshold level. In contrast, radical changes in the variable residue glutamic acid-167 (E167) had little or no effect on PapD function. These studies provide the first molecular details of how a periplasmic pilus chaperone binds to nascently translocated pilus subunits to guide their assembly into adhesive pili. 相似文献
5.
Yolande Bertin Jean-Pierre Girardeau Maurice Der Vartanian Christine Martin 《FEMS microbiology letters》1993,108(1):59-67
Abstract The putative chaperone-like protein ClpE, required for biogenesis of the Escherichia coli capsule-like antigen CS31A, was compared with ten known periplasmic chaperones from E. coli, Klebsiella pneumoniae, Bordetella pertussis, Haemophilus influenzae and Yersinia pestis . The amino acid sequence alignment was superimposed onto the three-dimensional structure of the PapD chaperone of uropathogenic E. coli , and amino acid residues involved in maintaining the structure integrity of the suggested binding site were found identical in most of the 11 chaperones. Construction of a phylogenetic tree to investigate the relationship within the chaperone family has revealed interesting degrees of relatedness between the different proteins. 相似文献
6.
In the search for the essential functional domains of the large mechanosensitive ion channel (MscL) of E. coli, we have cloned several mutants of the mscL gene into a glutathione S-transferase fusion protein expression system. The resulting mutated MscL proteins had either amino
acid additions, substitutions or deletions in the amphipathic N-terminal region, and/or deletions in the amphipathic central
or hydrophilic C-terminal regions. Proteolytic digestion of the isolated fusion proteins by thrombin yielded virtually pure
recombinant MscL proteins that were reconstituted into artificial liposomes and examined for function by the patch-clamp technique.
The addition of amino acid residues to the N-terminus of the MscL did not affect channel activity, whereas N-terminal deletions
or changes to the N-terminal amino acid sequence were poorly tolerated and resulted in channels exhibiting altered pressure
sensitivity and gating. Deletion of 27 amino acids from the C-terminus resulted in MscL protein that formed channels similar
to the wild-type, while deletion of 33 C-terminal amino acids extinguished channel activity. Similarly, deletion of the internal
amphipathic region of the MscL abolished activity. In accordance with a recently proposed spatial model of the MscL, our results
suggest that (i) the N-terminal portion participates in the channel activation by pressure, and (ii) the essential channel
functions are associated with both, the putative central amphipathic α-helical portion of the protein and the six C-terminal
residues RKKEEP forming a charge cluster following the putative M2 membrane spanning α-helix.
Received: 25 September 1996/Revised: 21 November 1996 相似文献
7.
Glutamine synthetase type I (GSI) genes have previously been described only in prokaryotes except that the fungus Emericella nidulans contains a gene (fluG) which encodes a protein with a large N-terminal domain linked to a C-terminal GSI-like domain. Eukaryotes generally contain
the type II (GSII) genes which have been shown to occur also in some prokaryotes. The question of whether GSI and GSII genes
are orthologues or paralogues remains a point of controversy. In this article we show that GSI-like genes are widespread in
higher plants and have characterized one of the genes from the legume Medicago truncatula. This gene is part of a small gene family and is expressed in many organs of the plant. It encodes a protein similar in size
and with between 36 and 46% amino acid sequence similarity to prokaryotic GS proteins used in the analyses, whereas it is
larger and with less than 25% similarity to GSII proteins, including those from the same plant species. Phylogenetic analyses
suggest that this protein is most similar to putative proteins encoded by expressed sequence tags of other higher plant species
(including dicots and a monocot) and forms a cluster with FluG as the most divergent of the GSI sequences. The discovery of
GSI-like genes in higher plants supports the paralogous evolution of GSI and GSII genes, which has implications for the use
of GS in molecular studies on evolution.
Received: 4 May 1999 / Accepted: 17 September 1999 相似文献
8.
Christine P. Piotte Airlie K. Hunter Craig J. Marshall Murray R. Grigor 《Journal of molecular evolution》1998,46(3):361-369
Three proteins have been identified in the milk of the common brush tail possum, Trichosurus vulpecula that from sequence analysis are members of the lipocalin family. They include β-lactoglobulin, which appears to have two
forms; a homologue to the late-lactation protein found in tammar, Macropus eugenii; milk; and a novel protein termed trichosurin. Whereas β-lactoglobulin and trichosurin are both expressed throughout lactation, the late-lactation protein is not detected
in samples taken before days 100–110 of lactation. The cDNAs encoding each of these proteins have been isolated from cDNA
libraries prepared using possum mammary mRNA and sequenced. Phylogenetic analysis showed that the T. vulpeculaβ-lactoglobulin, along with two other macropod β-lactoglobulins, forms a subclass of β-lactoglobulins distinct from those
for eutherian mammals; both marsupial late-lactation proteins appear to have similarities to a family of odorant-binding proteins,
whereas trichosurin has similarities to the major urinary proteins of rodents.
Received: 28 October 1996 / Accepted: 19 May 1997 相似文献
9.
We have isolated a 29,000-Da carbonic anhydrase (CA) protein from the zebrafish, Danio rerio, sequenced two peptide fragments, and tentatively identified it as a high-activity CA by inhibition kinetics. We have also
characterized a 1,537-bp message whose deduced sequence of 260 amino acids matches that of the isolated protein. This CA is
clearly an α-CA based on the similarity of its sequence to that of other members of the α-CA gene family. A phylogenetic analysis
suggested CAH-Z diverged after the branching of the CA-V and CA-VII genes and prior to the duplications that generated the
CA-I, CA-II, and CA-III genes of amniotes. This marks the first characterization of the mRNA and its protein product from
the CA gene of a teleost.
Received: 31 March 1996 / Accepted: 8 September 1996 相似文献
10.
Sequence Analyses and Phylogenetic Characterization of the ZIP Family of Metal Ion Transport Proteins 总被引:1,自引:0,他引:1
Several novel but similar heavy metal ion transporters, Zrt1, Zrt2, Zip1-4 and Irt1, have recently been characterized. Zrt1,
Zrt2 and Zip1-4 are probably zinc transporters in Saccharomyces cerevisiae and Arabidopsis thaliana whereas Irt1 appears to play a role in iron uptake in A. thaliana. The family of proteins including these functionally characterized transporters has been designated the Zrt- and Irt-related
protein (ZIP) family. In this report, ZIP family proteins in the current databases were identified and multiply aligned, and
a phylogenetic tree for the family was constructed. A family specific signature sequence was derived, and the available sequences
were analyzed for residues of potential functional significance. A fully conserved intramembranous histidyl residue, present
within a putative amphipathic, α-helical, transmembrane spanning segment, was identified which may serve as a part of an intrachannel
heavy metal ion binding site. The occurrence of a proposed extramembranal metal binding motif (H X H X H) was examined in
order to evaluate its potential functional significance for various members of the family. The computational analyses reported
in this topical review should serve as a guide to future researchers interested in the structure-function relationships of
ZIP family proteins.
Received: 31 March 1997/Revised: 14 May 1998 相似文献
11.
Summary. Phosphate transport in bacteria occurs via a phosphate specific transporter system (PSTS) that belongs to the ABC family of
transporters, a multisubunit system, containing an alkaline phosphatase. DING proteins were characterized due to the N-terminal
amino acid sequence DINGG GATL, which is highly conserved in animal and plant isolates, but more variable in microbes. Most
prokaryotic homologues of the DING proteins often have some structural homology to phosphatases or periplasmic phosphate-binding
proteins. In E. coli, the product of the inducible gene DinG, possesses ATP hydrolyzing helicase enzymic activity. An alkaline phosphorolytic enzyme of the PSTS system was purified
to homogeneity from the thermophilic bacterium Thermus thermophilus. N-terminal sequence analysis of this protein revealed the same high degree of similarity to DING proteins especially to
the human synovial stimulatory protein P205, the steroidogenesis-inducing protein and to the phosphate ABC transporter, periplasmic
phosphate-binding protein, putative (P. fluorescens Pf-5). The enzyme had a molecular mass of 40 kDa on SDS/PAGE, exhibiting optimal phosphatase activity at pH 12.3 and 70 °C.
The enzyme possessed characteristics of a DING protein, such as ATPase, ds endonuclease and 3′ phosphodiesterase (3′-exonuclease)
activities and binding to linear dsDNA, displaying helicase activity on supercoiled DNA. Purification and biochemical characterization
of a T. thermophilus DING protein was achieved. The biochemical properties, N-terminal sequence similarities of this protein implied that the
enzyme belongs to the PSTS family and might be involved in the DNA repair mechanism of this microorganism.
Authors’ address: Assist. Prof. A. A. Pantazaki, Laboratory of Biochemistry, Department of Chemistry, Aristotle University
of Thessaloniki, Thessaloniki 54124, Greece 相似文献
12.
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
13.
A Novel Family of Ubiquitous Heavy Metal Ion Transport Proteins 总被引:33,自引:0,他引:33
We describe a novel diverse family of metal ion transporter (CDF) proteins (the cation diffusion facilitator (CDF) family)
with members occurring in both prokaryotes and eukaryotes. Thirteen sequenced protein members of the CDF family have been
identified, several of which have been shown to transport cobalt, cadmium and/or zinc. All members of the CDF family possess
six putative transmembrane spanners with strongest conservation in the four N-terminal spanners, and on the basis of the analyses,
we present a unified structural model. Members of the family are shown to exhibit an unusual degree of size variation, sequence
divergence, and differences in cell localization and polarity. The phylogenetic tree for the CDF family reveals that prokaryotic
and eukaryotic proteins cluster separately. It allows functional predictions for some uncharacterized members of this family.
A signature sequence specific for the CDF family is derived.
Received: 15 July 1996/Revised: 21 October 1996 相似文献
14.
The Drosophila fat body protein 2 gene (Fbp2) is an ancient duplication of the alcohol dehydrogenase gene (Adh) which encodes a protein that differs substantially from ADH in its methionine content. In D. melanogaster, there is one methionine in ADH, while there are 51 (20% of all amino acids) in FBP2. Methionine is involved in 46% of amino
acid replacements when Fbp2 DNA sequences are compared between D. melanogaster and D. pseudoobscura. Methionine accumulation does not affect conserved residues of the ADH-ADHr-FBP2 multigene family. The multigene family has evolved by replacement of mildly hydrophobic amino acids by methionine with
no apparent reversion. Its short-term evolution was compared between two Drosophila species, while its long-term evolution was compared between two genera belonging respectively to acalyptrate and calyptrate
Diptera, Drosophila and Sarcophaga. The pattern of nucleotide substitution was consistent with an independent accumulation of methionines at the Fbp2 locus in each lineage. Under a steady-state model, the rate of methionine accumulation was constant in the lineage leading
to Drosophila, and was twice as fast as that in the calyptrate lineage. Substitution rates were consistent with a slight positive selective
advantage for each methionine change in about one-half of amino acid sites in Drosophila. This shows that selection can potentially account for a large proportion of amino acid replacements in the molecular evolution
of proteins.
Received: 12 December 1994 / Accepted: 15 April 1996 相似文献
15.
Molecular dissection of PapD interaction with PapG reveals two chaperone-binding sites 总被引:6,自引:2,他引:4
Zheng Xu C. Hal Jones David Haslam Jerome S. Pinkner Karen Dodson Jan Kihlberg Scott J. Hultgren 《Molecular microbiology》1995,16(5):1011-1020
P pili are composite adhesive fibres that allow uropathogenic Escherichia coli to gain a foothold in the host by binding to receptors present on the uroepithalium via the adhesin PapG. The assembly of P pili requires a periplasmic chaperone, PapD, that has an immunoglobulin-like three-dimensional structure. PapD-subunit complex formation involves a conserved anchoring mechanism in the chaperone cleft and a‘molecular zippering’to the extreme C-terminus of pilus subunits. A chaperone-binding assay was developed using fusions of the C-terminus of PapG to maltose-binding protein (MBP/G fusions) to investigate whether chaperone-subunit complex formation requires additional interactions. PapD bound strongly to an MBP/G fusion containing the C-terminal 140 amino acids of PapG (MBP/G175-314) but only weakly to the MBP/G234-314 fusion containing 81 C-terminal residues, arguing that the region between residues 175-234 contains additional information that is required for strong PapD-PapG interactions. PapD was shown to interact with a PapG C-terminal truncate containing residues 1-198 but not a truncate containing residues 1-145, suggesting the presence of a second, independent PapD interactive site. Four peptides overlapping the second site region were tested for binding to PapD in vitro to further delineate this motif. Only one of the peptides synthesized was recognized by PapD. The MBP/G fusion containing both binding sites formed a tight complex with PapD in vivo and inhibited pilus assembly by preventing chaperone-subunit complex formation. 相似文献
16.
A family of four satellite DNAs has been characterized in the genome of the bivalve mollusc, Donax trunculus. All share HindIII sites, a similar monomer length of about 160 base pairs (bp), and the related oligonucleotide motifs GGTCA and GGGTTA,
repeated six to 15 times within the repetitive units. The motif GGTCA is common to all members of the satellite family. It
is present in three of them in both orientations, interspersed within nonrepetitive DNA sequences. The hexanucleotide GGGTTA
appears to be the main building element of one of the satellites forming a prominent subrepeat structure in conjunction with
the 5-bp motif. The former has been also found in perfect tandem repeats in a junction region adjacent to the proper satellite
sequence. Southern analysis has revealed that (GGGTTA)n and/or related sequences are abundant and widely distributed in the D. trunculus genome. The distribution observed is consistent with the concurrence of the scattering of short sequence motifs throughout
the genome and the spread of longer DNA segments, with concomitant formation of satellite monomer repeats. Both kinds of dispersion
may have contributed to the observed complex arrangement of the HindIII satellite DNA family in Donax.
Received: 28 May 1996 / Accepted: 30 July 1996 相似文献
17.
Potenza N del Gaudio R Rivieccio L Russo GM Geraci G 《Journal of molecular evolution》2002,54(3):312-321
A novel member of the innexin family (cv-inx) has been isolated from the annelid polychaete worm Chaetopterus variopedatus using a PCR approach on genomic DNA and sequence analysis on genomic DNA clones. The gene is present in a HindIII-HindIII segment of 2250 bp containing an uninterrupted open reading frame of 1196 bp encoding a protein of 399 amino acids. The
predicted protein shows the typical structural features of innexins and consensus sites for phosphorylation. Analyses on genomic
DNA demonstrate that cv-inx is a single copy gene with no introns in the coding region, exactly corresponding to the cDNA
sequence. The gene expression is regulated during development as shown by Northern blots analyses of the RNA and by immunoreaction
with antibodies against the protein at several embryonic stages. The finding of an innexin in the phylum Annelida, outside
of the Ecdysozoa clade, and its peculiar gene structure suggest the necessity to reconsider the current hypothesis on the
origin and evolution of gap junctional proteins.
Received: 15 December 2000 / Accepted: 27 August 2001 相似文献
18.
Conserved immunoglobulin-like features in a family of periplasmic pilus chaperones in bacteria. 总被引:19,自引:2,他引:17 下载免费PDF全文
Detailed structural analyses revealed a family of periplasmic chaperones in Gram-negative prokaryotes which are structurally and possibly evolutionarily related to the immunoglobulin superfamily and assist in the assembly of adhesive pili. The members of this family have similar structures consistent with the overall topology of an immunoglobulin fold. Seven pilus chaperone sequences from Escherichia coli, Haemophilus influenzae and Klebsiella pneumoniae were aligned and their consensus sequence was superimposed onto the known three-dimensional structure of PapD, a representative member of the family. The molecular details of the conserved and variable structural motifs in this family of periplasmic chaperones give important insight into their structure, function, mechanism of action and evolutionary relationship with the immunoglobulin superfamily. 相似文献
19.
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
20.
Gerhard Schenk Roy Layfield Judith M. Candy Ronald G. Duggleby Peter F. Nixon 《Journal of molecular evolution》1997,44(5):552-572
Members of the transketolase group of thiamine-diphosphate-dependent enzymes from 17 different organisms including mammals,
yeast, bacteria, and plants have been used for phylogenetic reconstruction. Alignment of the amino acid and DNA sequences
for 21 transketolase enzymes and one putative transketolase reveals a number of highly conserved regions and invariant residues
that are of predicted importance for enzyme activity, based on the crystal structure of yeast transketolase. One particular
sequence of 36 residues has some similarities to the nucleotide-binding motif and we designate it as the transketolase motif.
We report further evidence that the recP protein from Streptococcus pneumoniae might be a transketolase and we list a number of invariant residues which might be involved in substrate binding. Phylogenies
derived from the nucleotide and the amino acid sequences by various methods show a conventional clustering for mammalian,
plant, and gram-negative bacterial transketolases. The branching order of the gram-positive bacteria could not be inferred
reliably. The formaldehyde transketolase (sometimes known as dihydroxyacetone synthase) of the yeast Hansenula polymorpha appears to be orthologous to the mammalian enzymes but paralogous to the other yeast transketolases. The occurrence of more
than one transketolase gene in some organisms is consistent with several gene duplications. The high degree of similarity
in functionally important residues and the fact that the same kinetic mechanism is applicable to all characterized transketolase
enzymes is consistent with the proposition that they are all derived from one common ancestral gene. Transketolase appears
to be an ancient enzyme that has evolved slowly and might serve as a model for a molecular clock, at least within the mammalian
clade.
Received: 13 September 1995 / Accepted: 14 November 1996 相似文献