Oligomerization of water and solute channels of the major intrinsic protein (MIP) family.

Water and small solute fluxes through cell membranes are ensured in many tissues by selective pores that belong to the major intrinsic protein family (MIP). This family includes the water channels or aquaporins (AQP) and the neutral solute facilitators such as the glycerol facilitator (GlpF). We have compared the characteristics of representatives of each subfamily. Following solubilization in the nondenaturing detergents n-octyl-glucoside (OG) and Triton X-100 (T-X100), AQPs remain in their native homotetrameric state, while GlpF always behaves as a monomer. Solute facilitators are fully solubilized by the detergent N-lauroyl sarcosine (NLS), while AQPs are not. Analyses of mutants and chimeras demonstrate a close correlation between the water transport function and the resistance to NLS solubilization. Thus, AQPs and solute facilitators exhibit different behaviors in mild detergents; this could reflect differences in quaternary organization within the membranes. We propose that the oligomerization state or the strength of self-association is part of the mechanisms used by MIP proteins to ensure solute selectivity.

Color and graphic display (CGD): programs for multiple sequence alignment analysis in spreadsheet software.

Interpretation of multiple sequence alignments is of major interest for the prediction of functional and structural domains in proteins or for the organization of related sequences in families and subfamilies. However, a necessity for the bench scientist is the use of outstanding programs in a friendly computing environment. This paper describes Color and Graphic Display (CGD), a set of modules that runs as part of the Microsoft Excel spreadsheet to color and analyze multiple sequence alignments. Discussed here are the main functions of CGD and the use of the program to highlight residues of importance in a water channel family. Although CGD was created for protein sequences, most of the modules are compatible with DNA sequences.

A symbolic-numeric approach to find patterns in genomes. Application to the translation initiation sites of E. coli.

DNA sequence data provided by genome sequencing programs open new research prospects. In this respect, computational investigations are of major importance to discover new 'functional/structural patterns' and to improve biological process knowledge. For example, even though the principal steps of translation initiation in prokaryotes are known, it is difficult to point out the exact pattern of the mRNA that is recognized by the ribosome. In this study, we have carried out a systematic context analysis of the complete genome of E. coli, around codons in competition for translation initiation. Using a combinatorial approach, we first show that it is possible to accurately define the initiation site by looking for the localization of patterns representing various combinations of trinucleotides. We have combined this approach with a statistical analysis based on the frequencies of these patterns. This leads to a decision tree, able to discriminate true and false starts with a recognition level near 90%. Our method may help to precisely localize the beginning of open reading frames, and point to likely mistakes for some genes in the database. The method may be included as a component of a gene recognition system, is not restricted to a particular genome or a two-classes discrimination, and may be applied to a broader class of biological patterns.

Visualization of AqpZ-mediated water permeability in Escherichia coli by cryoelectron microscopy.

Transport of water across the plasma membrane is a fundamental process occurring in all living organisms. In bacteria, osmotic movement of water across the cytoplasmic membrane is needed to maintain cellular turgor; however, the molecular mechanisms of this process are poorly defined. Involvement of aquaporin water channels in bacterial water permeability was suggested by the recent discovery of the aquaporin gene, aqpZ, in Escherichia coli. By employing cryoelectron microscopy to compare E. coli cells containing (AqpZ+) and lacking (AqpZ-) aquaporin, we show that the AqpZ water channel rapidly mediates large water fluxes in response to sudden changes in extracellular osmolarity. These findings (i) demonstrate for the first time functional expression of a prokaryotic water channel, (ii) evidence the bidirectional water channel feature of AqpZ, (iii) document a role for AqpZ in bacterial osmoregulation, and (iv) define a suitable model for studying the physiology of prokaryotic water transport.

Switch from an aquaporin to a glycerol channel by two amino acids substitution.

The MIP (major intrinsic protein) proteins constitute a channel family of currently 150 members that have been identified in cell membranes of organisms ranging from bacteria to man. Among these proteins, two functionally distinct subgroups are characterized: aquaporins that allow specific water transfer and glycerol channels that are involved in glycerol and small neutral solutes transport. Since the flow of small molecules across cell membranes is vital for every living organism, the study of such proteins is of particular interest. For instance, aquaporins located in kidney cell membranes are responsible for reabsorption of 150 liters of water/day in adult human. To understand the molecular mechanisms of solute transport specificity, we analyzed mutant aquaporins in which highly conserved residues have been substituted by amino acids located at the same positions in glycerol channels. Here, we show that substitution of a tyrosine and a tryptophan by a proline and a leucine, respectively, in the sixth transmembrane helix of an aquaporin leads to a switch in the selectivity of the channel, from water to glycerol.

Oligomerization state of MIP proteins expressed in Xenopus oocytes as revealed by freeze-fracture electron-microscopy analysis.

The MIP (major intrinsic protein) family is a widespread family of membrane proteins exhibiting two major types of channel properties: aquaporins and solute facilitators. In the present study, freeze-fracture electron microscopy was used to investigate the oligomerization state of two MIP proteins heterologously expressed in the plasma membrane of Xenopus laevis oocytes: AQPcic, an aquaporin from the insect Cicadella viridis, and GlpF, a glycerol facilitator from Escherichia coli. Swelling assays performed on oocytes 48 and 72 h following cRNA microinjections showed that these proteins were functionally expressed. Particle density determinations indicated that expression of proteins is related to an increase in particle density on the P fracture face of oocyte plasma membranes. Statistical analysis of particle sizes was performed on protoplasmic fracture faces of the plasma membrane of oocytes expressing AQPcic and GlpF 72 h after cRNA microinjections. Compared to control oocytes, AQPcic-expressing oocytes exhibited a specific population of particles with a mean diameter of 8.7 +/- 0.1 nm. This value is consistent with the previously reported tetrameric organization of AQPcic. In addition, AQPcic particles aggregate and form orthogonal arrays similar to those observed in native membranes of C. viridis, consisting of homotetramers of AQPcic. On the protoplasmic fracture face of oocytes expressing GlpF, the particle density is increased by 4.1-fold and the mean diameter of specifically added particles is 5.8 +/- 0.1 nm. This value fits with a monomer of the 28-kDa GlpF protein plus the platinum-carbon layer. These results clearly demonstrate that GlpF is a monomer when functionally expressed in plasma membranes of Xenopus oocytes and therefore emphasize the key role of the oligomerization state of MIP proteins with respect to their function.

Oligomerization state of water channels and glycerol facilitators. Involvement of loop E.

The major intrinsic protein (MIP) family includes water channels aquaporins (AQPs) and facilitators for small solutes such as glycerol (GlpFs). Velocity sedimentation on sucrose gradients demonstrates that heterologous AQPcic expressed in yeast or Xenopus oocytes behaves as an homotetramer when extracted by n-octyl beta-D-glucopyranoside (OG) and as a monomer when extracted by SDS. We performed an analysis of GlpF solubilized from membranes of Escherichia coli or of mRNA-injected Xenopus oocytes. The GlpF protein extracted either by SDS or by nondenaturing detergents, OG and Triton X-100, exhibits sedimentation coefficients only compatible with a monomeric form of the protein in micelles. We then substituted in loop E of AQPcic two amino acids predicted to play a role in the functional/structural properties of the MIPs. In two expression systems, yeast and oocytes, the mutant AQPcic-S205D is monomeric in OG and in SDS. The A209K mutation does not modify the tetrameric form of the heterologous protein in OG. This study shows that the serine residue at position 205 is essential for AQPcic tetramerization. Because the serine in this position is highly conserved among aquaporins and systematically replaced by an acid aspartic in GlpFs, we postulate that glycerol facilitators are monomers whereas aquaporins are organized in tetramers. Our data suggest that the role of loop E in MIP properties partly occurs through its ability to allow oligomerization of the proteins.

Prediction of functional residues in water channels and related proteins.

In this paper, we present an updated classification of the ubiquitous MIP (Major Intrinsic Protein) family proteins, including 153 fully or partially sequenced members available in public databases. Presently, about 30 of these proteins have been functionally characterized, exhibiting essentially two distinct types of channel properties: (1) specific water transport by the aquaporins, and (2) small neutral solutes transport, such as glycerol by the glycerol facilitators. Sequence alignments were used to predict amino acids and motifs discriminant in channel specificity. The protein sequences were also analyzed using statistical tools (comparisons of means and correspondence analysis). Five key positions were clearly identified where the residues are specific for each functional subgroup and exhibit high dissimilar physico-chemical properties. Moreover, we have found that the putative channels for small neutral solutes clearly differ from the aquaporins by the amino acid content and the length of predicted loop regions, suggesting a substrate filter function for these loops. From these results, we propose a signature pattern for water transport.

Molecular cloning and characterization of an insect aquaporin functional comparison with aquaporin 1.

We previously described the structural organization of P25, a member of the major-intrinsic-protein family found in the digestive tract of homopteran sap-sucking insects [Beuron, F., Le Cahérec, F., Guillam, M. T., Cavalier, A., Garret, A., Tassan, J. P., Delamarche, C., Schultz, P., Mallouh, V., Rolland, J. P., Hubert, J.F., Gouranton, J. & Thomas, D. (1995) J. Biol. Chem. 270, 17414-17422]. We demonstrated, by means of introducing P25 tetramers into the membranes of Xenopus oocytes, that this protein exhibits functional properties similar to those of aquaporin 1, the archetypal water channel [Le Cahérec, F., Bron, P., Verbavatz, J. M., Garret, A., Morel, G., Cavalier, A., Bonnec, G., Thomas, D., Gouranton, J. & Hubert, J.F. (1996) J. Cell Sci. 109, 1285-1295]. In the present work, we cloned a full-length cDNA from a Cicadella viridis library with an open reading frame of 765 bp that encoded a 26-kDa protein whose sequence was 43, 40, 36 and 36% identical to aquaporins 1, 2, z and tonoplast intrinsic protein gamma, respectively. Translation of the corresponding RNA in Xenopus oocytes generated a polypeptide that was specifically recognized by polyclonal antibodies raised against native P25. Expression of the protein in Xenopus oocyte membranes was assessed by immunocytochemistry and led to a 15-fold increase of osmotic membrane water permeability. This increase was inhibited by HgCl2. The permeability had an Arrhenius activation energy of 11.7 kJ/mol. We called this protein Cicadella aquaporin (AQPcic). The oocytes expressing Cicadella aquaporin were less sensitive to HgCl2 than oocytes expressing aquaporin 1. In the Xenopus oocyte system, Cicadella aquaporin failed to transport glycerol, urea and ions. It exhibited permeabilities to ethylene glycol and formamide similar to those measured for aquaporin 1 under the same conditions.

Characterization of the Pasteurella multocida skp and firA genes.

A 2.9-kb fragment of the Pasteurella multocida (Pm) genome encoding proteins p25 (25 kDa) and p28 (28 kDa) has previously been cloned and expressed in Escherichia coli (Ec). In the present paper, the nucleotide (nt) sequence of a 1.8-kb subfragment encoding the two proteins is described. The cloned fragment contains three open reading frames (ORFs). ORF1 is incomplete. ORF2 is homologous to the skp gene of Ec. ORF3 overlaps ORF2 and is highly homologous to the firA gene of Ec. The skp and firA genes are part of an operon governing the first steps of lipid A synthesis. Comparing the nt sequence with the N-terminal sequences of p25 and p28 revealed that the two proteins are encoded by ORF2 (skp). The preprotein p28 is converted into p25 by cleavage of a 23-amino-acid leader peptide. Though it serologically cross-reacts with porin H of Pm, p25 is not related to known bacterial porins.

Structural analysis of a MIP family protein from the digestive tract of Cicadella viridis.

Homopteran insects, and especially Cicadella viridis, display in their digestive tract a specialized epithelial differentiation, the filter chamber (FC) acting as a water-shunting complex. The main intrinsic membrane protein of the FC is a 25,000-Da polypeptide (P25). In this paper we demonstrate that this P25 polypeptide is a member of the MIP family of membrane channel proteins, and that P25 forms homotetramers in the native membranes. Using polymerase chain reaction, a 360-base pair cDNA, named cic, was isolated from RNA of the FC. cic encodes a 119-amino acid polypeptide (CIC) whose homologies with MIP26, AQP1 (CHIP), AQP2, and gamma-TIP are 38, 38, 34, and 20%, respectively. Using a specific antibody raised against a 15-amino acid peptide from the CIC sequence, we concluded that CIC and P25 are identical entities, and hence that P25 belongs to the MIP family. We investigated the quaternary structure of P25 in the membranes of the FC using biophysical analysis of P25 nondenaturing detergent micelles, scanning transmission electron microscopy, and image processing of conventional transmission electron microscopic images. All those different approaches converged to the conclusion that P25 exists as an homotetramer forming a regular two-dimensional array in the membranes.

Cloning and expression of two Pasteurella multocida genes in Escherichia coli.

A library of cloned Pasteurella multocida (toxigenic strain 9222, serotype D2) genomic sequences was constructed in Escherichia coli by incorporating TaqI digestion fragments into the plasmid vector pUC19. Immunological screening with antibodies directed against porin H, the major protein of the P multocida outer membrane, allowed the identification of a recombinant plasmid containing a 2.9-kbp DNA insert. This plasmid encoded the synthesis of two polypeptides, p25 (25 kDa) and p28 (28 kDa) which were detected in the different compartments of the E coli transformant. The peptide p25 was more abundant in the periplasm whereas p28 was mainly found in the cell envelope and in the cytosol. Immunological analysis indicates that p25, in contrast to p28, is antigenically related to porin H of P multocida. The expression in E coli of the gene encoding p28 was enhanced by induction of the lac promoter.

Protein IIIa of Rhizobium leguminosarum is probably a porin.

The cloning, sequencing and expression of the gene encoding the 36-kilodalton (kDa) outer membrane protein of Rhizobium leguminosarum has been recently described in the literature (De Maagd RA et al (1992) J Bacteriol 174, 214-221). We present evidence that this protein is a porin from a sub-type covalently bound to the peptidoglycan.

Aging and Alzheimer's disease: protease inhibitors in cerebrospinal fluid.

Recent advances suggested that proteases and their inhibitors could be implicated in the genesis and/or maturation of insoluble deposits associated with Alzheimer's disease (AD). This study was designed to measure the level of alpha 1-antichymotrypsin (ACT) and alpha 1-antitrypsin (AT) in cerebrospinal fluid (CSF) of patients with AD and nondemented humans at various ages. Our analysis failed to demonstrate a significant relationship between inhibitor content and disease. However, a positive correlation was observed between age and the ACT level for the normal control group. Such observation suggests a specific association of ACT with the mechanisms of brain aging.

[Does spiralin has a cleavable N-terminal signal sequence?]. / La spiraline possède-t-elle une séquence signal N-terminale clivable?

The amino acid sequence of spiralin deduced from the nucleotide sequence of its gene was fictitiously shortened by 1 to 50 residues from each terminus and the compositions of both series of theoretical polypeptides were calculated. The two series of compositions thus obtained were compared to that of the purified protein, with the use of the Marchalonis and Weltman index (S delta Q). The results of this analysis, which permits the difficulty resulting from the blocking of the N-terminal amino acid to be overcome, show that spiralin is probably synthesized as a 241-residue precursor containing an N-terminal signal sequence cleaved close to cysteine-24. Since spiralin is acylated and since the sequence Val-Val-Ala-Cys24 shares some similarity with the consensus sequence of bacterial lipoprotein modification/processing site, the hypothesis of a cleavage just before cysteine-24 seems plausible.

A homologous domain between the amyloid protein of Alzheimer's disease and the neurofilament subunits.

Polypeptide (A4), which is derived from a larger precursor membrane protein (beta APP), is an important component of brain amyloid in Alzheimer's disease. The physiological function and the processing of this precursor are largely unknown. In order to elucidate the actual role of beta APP, we searched for domain homology with other proteins. The present study reveals the presence of a highly conserved region between the amyloid precursor and the 3 neurofilament subunits. Identical amino acids are present at about 45% of the positions aligned between the 4 sequences. These observations are discussed in terms of a possible involvement of positive ions in the maturation of these proteins and are in favour the implication of aluminium in Alzheimer's disease.

An ELISA technique for the measurement of C1q in cerebrospinal fluid.

Determination of the C1q content of cerebrospinal fluid (CSF) may be of value in understanding the immunological reactions occurring within the central nervous system (CNS). A double sandwich ELISA method has been developed for the detection of C1q in human serum and CSF. It uses polyclonal antibodies and is sensitive in the nanogram range. The mean concentrations of C1q were determined to be 127 micrograms/ml in serum and 0.4 microgram/ml in CSF. These results suggest that increased levels of C1q in the CSF play a role in some neurodegenerative disorders.

Mutants affecting tRNA(Phe) from Escherichia coli. Studies of the suppression of thermosensitive phenylalanyl-tRNA synthetase.

Four mutants of pheV, a gene coding for tRNA(Phe) in Escherichia coli, share the characteristic that when carried in the plasmid pBR322, they lose the capacity of wild-type pheV to complement the thermosensitive defect in a mutant of phenylalanyl-tRNA synthetase. One of these mutants, leading to the change C2----U2 in tRNA(Phe), is expressed about 10-fold lower in transformed cells than wild-type pheV. This mutant, unlike the remaining three (G15----A15, G44----A44, m7G46----A46), can recover the capacity to complement thermosensitivity when carried in a plasmid of higher copy number. The other three mutants, even when expressed at a similar level, remain unable to complement thermosensitivity. A study of charging kinetics suggests that the loss of complementation associated with these mutants is due to an altered interaction with phenylalanyl-tRNA synthetase. The mutant gene pheV (U2), when carried in pBR322, can also recover the capacity to complement thermosensitivity through a second-site mutation outside the tRNA structural gene, in the discriminator region. This mutation, C(-6)----T(-6), restores expression of the mutant U2 to about the level of wild-type tRNA(Phe).

Does UGA suppressor tRNATrp from Escherichia coli have a unique CCA anticodon sequence?

The properties of the UGA-suppressor tRNATrp (anticodon CCA) from Escherichia coli has greatly influenced ideas about the specificity of codon-anticodon interactions showing that the anticodon sequence is not the sole determinant. However, a recent hypothesis for the mechanism of suppression by this tRNA proposes that the base change in position 24, in the dihydrouridine stem, leads to a change in translational specificity of the tRNA by increasing post-transcriptional modification of cytidine 34, in the anticodon wobble position [M. Yarus (1982) Science (Wash. DC) 218, 646-652]. The enzyme postulated to do this normally modifies C34 of a minor isoleucine isoacceptor specific for AUA codons. This modification should reduce reading of G in the third codon position: affinity chromatography on columns containing immobilised tRNAPro (anticodon VGG) has therefore been employed to isolate an enriched population of the putative suppressor species, if such a sub-population exists. The results obtained are difficult to reconcile with the presence of a subfraction, modified post-transcriptionally in C34, responsible for the suppression of UGA. This argues in favour of the previously advanced hypothesis for the mechanism of suppression, which depends on events outside the codon-anticodon interaction itself.