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1.
2.
Microbial Relatives of Seed Storage Proteins: Conservation of Motifs in a Functionally Diverse Superfamily of Enzymes 总被引:1,自引:0,他引:1
Plant storage proteins comprise a major part of the human diet. Sequence analysis has revealed that these proteins probably
share a common ancestor with a fungal oxalate decarboxylase and/or related bacterial genes. Additionally, all these proteins
share a central core sequence with several other functionally diverse enzymes and binding proteins, many of which are associated
with synthesis of the extracellular matrix during sporulation/encystment. A possible prokaryotic relative of this sequence
is a bacterial protein (SASP) known to bind to DNA and thereby protect spores from extreme environmental conditions. This
ability to maintain cell viability during periods of dehydration in spores and seeds may relate to absolute conservation of
residues involved in structure determination.
Received: 25 April 1997 / Accepted: 29 July 1997 相似文献
3.
We combined widely different biochemical methods to analyze proteins of the cell surface of P. tetraurelia since so far one can isolate only a subfraction of cell membrane vesicles enriched in the GPI-anchored surface antigens (``immoblization'
or ``i-AGs'). We also found that i-AGs may undergo partial degradation by endogenous proteases. Genuine intrinsic membrane
proteins were recognized particularly with lipophilic 5-[125I]-iodonaphthalene-1-azide (INA) labeling which reportedly ``sees' integral proteins and cytoplasmic cell membrane-associated
proteins. With INA (+DTT), bands of ≤55 kDa were similar as with hydrophilic iodogen (+DTT), but instead of large size bands
including i-AGs, a group of 122, 104 and 94 kDa appeared. Several bands of the non i-AG type are compatible with integral
(possibly oligomeric) or associated proteins of the cell membrane of established molecular identity, as we discuss. In summary,
we can discriminate between i-AGs and some functionally important minor cell membrane components. Our methodical approach
might be relevant also for an analysis of some related protozoan parasites.
Received: 5 April 1999/Revised: 19 July 1999 相似文献
4.
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
5.
6.
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
7.
The sodium bicarbonate cotransporter (NBC1) is essential for bicarbonate transport across plasma membranes in epithelial
and nonepithelial cells. The direction of the NaHCO3 movement in secretory epithelia is opposite to that in reabsorptive epithelia. In secretory epithelia (such as pancreatic
duct cells) NBC is responsible for the transport of bicarbonate from blood to the cell for eventual secretion at the apical
membrane. In reabsorptive epithelia (such as kidney proximal tubule cells) NBC is responsible for the reabsorption of bicarbonate
from cell to the blood. In nonepithelial cells this transporter is mainly involved with cell pH regulation. Recent molecular
cloning experiments have identified the existence of four NBC isoforms (NBC1, 2, 3 and 4) and two NBC-related proteins AE4
and NCBE (Anion Exchanger 4 and Na-dependent Chloride-Bicarbonate Exchanger). All but AE4 are presumed to mediate the cotransport
of Na+ and HCO3
− under normal conditions and may be functionally altered in certain pathologic states. NBC1 shows a limited tissue expression
pattern, is electrogenic and plays an important role in bicarbonate reabsorption in kidney proximal tubule. In addition to
the kidney, NBC1 is expressed in pancreatic duct cells, is activated by cystic fibrosis transmembrane conductance regulator
(CFTR) and plays an important role in HCO3
− secretion. NBC2 and NBC3 have a wider tissue distribution than NBC1, are electroneutral, and are involved with cell pH regulation.
The characterization of NBC4 is incomplete. The NBC-related protein called NCBE mediates Na-dependent, Cl−/Bicarbonate Exchange. The purpose of this review is to summarize recent advances on the cloning of NBC isoforms and related
proteins and their role and regulation in physiologic and pathologic states.
Received: 26 February 2001/Revised: 14 May 2001 相似文献
8.
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
9.
Traebert M Köhler K Lambert G Biber J Forster I Murer H 《The Journal of membrane biology》2001,180(1):83-90
We have combined a functional assay, surface labeling and immunocytochemical methods to compare total and surface-exposed
renal type IIa Na+/P
i
cotransporter protein. The wild-type type cotransporter (NaPi-IIa) and its functionally comparable cysteine mutant S460C
were expressed in Xenopus oocytes. S460C contains a novel cysteine residue that, when modified by preincubation with methanethiosulfonate reagents,
leads to complete suppression of cotransport function. This allowed surface labeling of the S460C using MTSEA-Biotin and confirmation
by electrophysiology on the same cell. Protein was analyzed by Western blotting before and after streptavidin precipitation
and by immunocytochemistry and immunogold electronmicroscopy. MTSEA-Biotin treatment resulted in a complete inhibition of
S460C-mediated Na+/P
i
-cotransport activity, which indicated that all transporters at the surface were biotinylated. After biotinylation, only a
small fraction of total S460C protein was precipitated by streptavidin compared with the total amount of S460C protein detected
in the lysate. Light- and electron-microscopy analysis of oocytes showed a large amount of WT and S460C transporter protein
beneath the oocyte membrane. These data indicate that the apparent weak labeling efficiencies of surface-biotinylation-based
assays of membrane proteins heterologously expressed in oocytes can be related to diminished incorporation of the protein
in the oolemma.
Received: 18 August 2000/Revised: 1 December 2000 相似文献
10.
The rat renal Na/P
i
cotransporter type IIa (rat NaPi IIa) is a 637 amino acid protein containing 12 cysteine residues. We examined the effect of different cysteine modifying
methanethiosulfonate (MTS)-reagents and the disulfide bond reducing agent tris(2-carboxyethyl)phosphine (TCEP) on the transport
activity of wild-type and 12 single cysteine substitution mutants of rat NaPi IIa expressed in Xenopus laevis oocytes. The transport activity of the wild-type protein was resistant to three membrane impermeant MTS-reagents (MTSEA,
MTSET and MTSES). In contrast, membrane permeant methyl methanethiosulfonate (MMTS) and TCEP inhibited the transport activity
of both the wild-type, as well as all the single mutant proteins. This indicated the existence of more than one functionally
important cysteine residue, not accessible extracellularly, and at least 2 disulfide bridges. To identify the disulfide bridges,
three double mutants lacking 2 of the 3 cysteine residues predicted to be extracellular in different combinations were examined.
This led to the identification of one disulfide bridge between C306 and C334; reconsideration of the topological model predictions
suggested a second disulfide bridge between C225 and C520. Evaluation of a fourth double mutant indicated that at least one
of two disulfide bridges (C306 and C334; C225 and C520) has to be formed to allow the surface expression of a functional cotransporter.
A revised secondary structure is proposed which includes two partially repeated motifs that are connected by disulfide bridges
formed between cysteine pairs C306-C334 and C225-C520.
Received: 13 December 1999/Revised: 31 March 2000 相似文献
11.
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
12.
Insect vitellogenin and yolk protein receptors (VgR/YPR) are newly discovered members of the low-density lipoprotein receptor
(LDLR) family, which is characterized by a highly conserved arrangement of repetitive modular elements homologous to functionally
unrelated proteins. The insect VgR/YPRs are unique in having two clusters of complement-type cysteine-rich (class A) repeats
or modules, with five modules in the first cluster and seven in the second cluster, unlike classical LDLRs which have a single
seven-module cluster, vertebrate VgRs and very low density lipoprotein receptors (VLDLR) which have a single eight-module
cluster, and LDLR-related proteins (LRPs) and megalins which have four clusters of 2–7, 8, 10, and 11 modules. Alignment of
clusters across subfamilies by conventional alignment programs is problematic because of the repetitive nature of the component
modules which may have undergone rearrangements, duplications, and deletions during evolution. To circumvent this problem,
we ``fingerprinted' each class A module in the different clusters by identifying those amino acids that are both relatively
conserved and relatively unique within the cluster. Intercluster reciprocal comparisons of fingerprints and aligned sequences
allowed us to distinguish four cohorts of modules reflecting shared recent ancestry. All but two of the 57 modules examined
could be assigned to one of these four cohorts designated A, B, C, and D. Alignment of clusters based on modular cohorts revealed
that all clusters are derived from a single primordial cluster of at least seven modules with a consensus arrangement of CDCADBC.
All extant clusters examined are consistent with this consensus, though none matches it perfectly. This analysis also revealed
that the eight-module clusters in vertebrate VgRs, insect VgR/YPRs, and LRP/megalins are not directly homologous with one
another. Assignment of modules to cohorts permitted us to properly align 32 class A clusters from all four LDLR subfamilies
for phylogenetic analysis. The results revealed that smaller one-cluster and two-cluster members of the family did not originate
from the breakup of a large two-cluster or four-cluster receptor. Similarly, the LRP/megalins did not arise from the duplication
of a two-cluster insect VgR/YPR-like progenitor. Rather, it appears that the multicluster receptors were independently constructed
from the same single-cluster ancestor.
Received: 16 January 1997 / Accepted: 21 August 1997 相似文献
13.
14.
The sequences of the entire blue opsin gene in the squirrel monkey (Saimiri boliviensis) and the five introns of the human blue opsin gene were obtained. Intron 3 of these genes contains an Alu sequence and intron
4 contains a partial mer13 sequence. A comparison of the squirrel monkey opsin sequence with published mammalian opsin sequences
shows that features believed to be functionally critical are all conserved. However, the blue opsin has evolved twice as fast
as rhodopsin and is only as conservative as the β globin, which has evolved at the average rate of mammalian proteins. Interestingly,
the interhelical loops are, on average, actually more conservative than the transmembrane α helical regions. The introns of
the blue opsin gene have evolved at the average rate of introns in primate genes.
Received: 5 August 1996 / Accepted: 2 October 1996 相似文献
15.
Vegetative cells of the filamentous ascomycete Neurospora tetrasperma are typically heterokaryotic, possessing haploid nuclei of both A and a mating types. As a consequence, N. tetrasperma is self-fertile. This life cycle, referred to as pseudohomothallism, clearly derives from true heterothallism of the type
exhibited by related species such as N. crassa. Occasional homokaryotic, single-mating-type (heterothallic) isolates occur; in the laboratory, such strains can be outcrossed.
The potential for outcrossing in N. tetrasperma raises the question of how this organism avoids heterokaryon incompatibility. Heterokaryon incompatability in vegetatively
growing fungi is controlled by multiple loci. Two strains must be identical at each het locus (11 in N. crassa) to form a stable heterokaryon. Prior to the present survey, it seemed plausible that N. tetrasperma avoids heterokaryon incompatibility by maintaining compatible allele combinations through continual selfing. A survey of
het-c variation among wild-type isolates in this study demonstrated that N. tetrasperma outcrosses in nature and that such matings can result in incompatible combinations of het-c alleles. Whereas individual wild-type isolates are invariably homoallelic for het-c, closely related strains may possess functionally different het-c alleles, which predate the origin of N. tetrasperma. Therefore, pseudohomothallic ascomycetes such as N. tetrasperma face an apparent evolutionary dilemma: the benefits of outcrossing must be balanced against the fact that matings can produce
unstable heterokaryons and disrupt the pseudohomothallic life cycle.
Received: 22 October 1999 / Accepted: 7 September 2000 相似文献
16.
Herdman M Coursin T Rippka R Houmard J Tandeau de Marsac N 《Journal of molecular evolution》2000,51(3):205-213
The evolutionary origin of the phytochromes of eukaryotes is controversial. Three cyanobacterial proteins have been described
as ``phytochrome-like' and have been suggested to be potential ancestors of these essential photoreceptors: Cph1 from Synechocystis PCC 6803, showing homology to phytochromes along its entire length and known to attach a chromophore; and PlpA from Synechocystis PCC 6803 and RcaE from Fremyella diplosiphon, both showing homology to phytochromes most strongly only in the C-terminal region and not known to bind a chromophore. We
have reexamined the evolution of the photoreceptors using for PCR amplification a highly conserved region encoding the chromophore-binding
domain in both Cph1 and phytochromes of plants and have identified genes for phytochrome-like proteins (PLP) in 11 very diverse
cyanobacteria. The predicted gene products contain either a Cys, Arg, Ile, or Leu residue at the putative chromophore binding
site. In 10 of the strains examined only a single gene was found, but in Calothrix PCC 7601 two genes (cphA and cphB) were identified. Phylogenetic analysis revealed that genes encoding PLP are homologues that share a common ancestor with
the phytochromes of eukaryotes and diverged before the latter. In contrast, the putative sensory/regulatory proteins, including
PlpA and RcaE, that lack a part of the chromophore lyase domain essential for chromophore attachment on the apophytochrome,
are only distantly related to phytochromes. The Ppr protein of the anoxygenic photosynthetic bacterium Rhodospirillum centenum and the bacterial phytochrome-like proteins (BphP) of Deinococcus radiodurans and Pseudomonas aeruginosa fall within the cluster of cyanobacterial phytochromes.
Received: 9 December 1999 / Accepted: 10 May 2000 相似文献
17.
The ubiquitous major intrinsic protein (MIP) family includes several transmembrane channel proteins known to exhibit specificity
for water and/or neutral solutes. We have identified 84 fully or partially sequenced members of this family, have multiply
aligned over 50 representative, divergent, fully sequenced members, have used the resultant multiple alignment to derive current
MIP family-specific signature sequences, and have constructed a phylogenetic tree. The tree reveals novel features relevant
to the evolutionary history of this protein family. These features plus an evaluation of functional studies lead to the postulates:
(i) that all current MIP family proteins derived from two divergent bacterial paralogues, one a glycerol facilitator, the
other an aquaporin, and (ii) that most or all current members of the family have retained these or closely related physiological
functions.
Received: 19 April 1996/Revised: 3 June 1996 相似文献
18.
The Origin of Chlorarachniophyte Plastids, as Inferred from Phylogenetic Comparisons of Amino Acid Sequences of EF-Tu 总被引:4,自引:0,他引:4
Ken-ichiro Ishida Ying Cao Masami Hasegawa Norihiro Okada Yoshiaki Hara 《Journal of molecular evolution》1997,45(6):682-687
A molecular phylogenetic analysis of elongation factor Tu (EF-Tu) proteins from plastids was performed in an attempt to identify
the origin of chlorarachniophyte plastids, which are considered to have evolved from the endosymbiont of a photosynthetic
eukaryote. Partial sequences of the genes for plastid EF-Tu proteins (1,080–1,089 bp) were determined for three algae that
contain chlorophyll b, namely, Gymnochlora stellata (Chlorarachniophyceae), Bryopsis maxima (Ulvophyceae), and Pyramimonas disomata (Prasinophyceae). The deduced amino acid sequences were used to construct phylogenetic trees of the plastid and bacterial
EF-Tu proteins by the maximum likelihood, the maximum parsimony, and the neighbor joining methods.
The trees obtained in the present analysis suggest that all plastids that contain chlorophyll b are monophyletic and that the chlorarachniophyte plastids are closely related to those of the Ulvophyceae. The phylogenetic
trees also suggest that euglenophyte plastids are closely related to prasinophycean plastids. The results indicate that the
chlorarachniophyte plastids evolved from a green algal endosymbiont that was closely related to the Ulvophyceae and that at
least two secondary endosymbiotic events have occurred in the lineage of algae with plastids that contain chlorophyll b.
Received: 10 March 1997 / Accepted: 28 July 1997 相似文献
19.
Patrick J. Babin Jan Bogerd Frank P. Kooiman Wil J. A. Van Marrewijk Dick J. Van der Horst 《Journal of molecular evolution》1999,49(1):150-160
Large lipid transfer proteins (LLTP) are nonexchangeable apolipoproteins and intracellular lipid-exchange proteins involved
in the assembly, secretion, and metabolism of lipoproteins. We have identified contiguous conserved sequence motifs in alignments
of insect apolipophorin II/I precursor (apoLp-II/I), human apolipoprotein B (apoB), invertebrate and vertebrate vitellogenins
(VTG), and the large subunit of mammalian microsomal triglyceride transfer protein (MTP). Conserved motifs present in the
N-terminal part of nonexchangeable apolipoproteins encompass almost completely the large subunit of MTP, suggesting a derivation
from a common ancestral functional unit, termed large lipid transfer (LLT) module. Divergence of LLTP from a common ancestor
is supported by (1) the statistical significance of the combined match scores obtained after motif-based database searches,
(2) the presence of several identical amino acid residues in all LLTP sequences currently available, (3) the conservation
of hydrophobic clusters in an α-helical domain, (4) the phylogenetic analysis of the conserved sequences related to the von
Willebrand factor D (VWD) module identified in nonexchangeable apolipoproteins, and (5) the presence of four and one ancestral
exon boundaries in the LLT and VWD modules, respectively. Our data indicate that the genes coding for apoLp-II/I, apoB, VTG,
and the MTP large subunit are members of the same multigene superfamily. LLTP have emerged from an ancestral molecule designed
to ensure a pivotal event in the intracellular and extracellular transfer of lipids and liposoluble substances.
Received: 8 June 1998 / Accepted: 15 February 1999 相似文献
20.