Functional Importance of GGXG Sequence Motifs in Putative Reentrant Loops of 2HCT and ESS Transport Proteins

Slipknotted and unknotted monovalent cation-proton antiporters evolved from a common ancestor

While the slipknot topology in proteins has been known for over a decade, its evolutionary origin is still a mystery. We have identified a previously overlooked slipknot motif in a family of two-domain membrane transporters. Moreover, we found that these proteins are homologous to several families of unknotted membrane proteins. This allows us to directly investigate the evolution of the slipknot motif. Based on our comprehensive analysis of 17 distantly related protein families, we have found that slipknotted and unknotted proteins share a common structural motif. Furthermore, this motif is conserved on the sequential level as well. Our results suggest that, regardless of topology, the proteins we studied evolved from a common unknotted ancestor single domain protein. Our phylogenetic analysis suggests the presence of at least seven parallel evolutionary scenarios that led to the current diversity of proteins in question. The tools we have developed in the process can now be used to investigate the evolution of other repeated-domain proteins.

In proteins with the slipknot topology, the polypeptide chain forms a slipknot—a structure that is not necessarily manifest to a naked eye, but it can be detected using mathematical methods. Slipknots are conserved motifs often found at catalytic sites and are directly involved in molecular transport. Although the first proteins with slipknots were found in 2007, many questions remain unanswered, e.g. how these proteins appeared, or whether the slipknotted proteins evolved from unknotted ones or vice versa. Here we provide the first analysis of homologous slipknotted and unknotted transmembrane proteins in order to elucidate their evolutionary relationship. We show that two-domain slipknotted and unknotted membrane transporters share the same one-domain unknotted protein as an ancestor. The ancestor gene duplicated and underwent various diversification and fusion events during the evolution, which have led to the appearance of a large superfamily of secondary active transporters. The slipknot motif seems to have been created by chance after a fusion of two single domain genes. Therefore, we show here that the slipknotted transporter evolved from an unknotted one-domain protein and that there are at least seven different evolutionary scenarios that gave rise to this large superfamily of transporters.

Structural insights into the elevator-like mechanism of the sodium/citrate symporter CitS

The sodium-dependent citrate transporter of Klebsiella pneumoniae (KpCitS) belongs to the 2-hydroxycarboxylate transporter (2-HCT) family and allows the cell to use citrate as sole carbon and energy source in anaerobic conditions. Here we present crystal structures of KpCitS in citrate-bound outward-facing, citrate-bound asymmetric, and citrate-free inward-facing state. The structures reveal that the KpCitS dimerization domain remains stationary throughout the transport cycle due to a hydrogen bond network as well as extensive hydrophobic interactions. In contrast, its transport domain undergoes a ~35° rigid-body rotation and a ~17 Å translocation perpendicular to the membrane to expose the substrate-binding site alternately to either side of the membrane. Furthermore, homology models of two other 2-HCT proteins based on the KpCitS structure offer structural insights into their differences in substrate specificity at a molecular level. On the basis of our results and previous biochemical data, we propose that the activity of the 2-HCT CitS involves an elevator-like movement in which the transport domain itself traverses the lipid bilayer, carrying the substrate into the cell in a sodium-dependent manner.

Structure and elevator mechanism of the Na+-citrate transporter CitS

The recently determined crystal structure of the bacterial Na⁺-citrate symporter CitS provides unexpected structural and mechanistic insights. The protein has a fold that has not been seen in other proteins, but the oligomeric state, domain organization and proposed transport mechanism strongly resemble those of the sodium-dicarboxylate symporter vcINDY, and the putative exporters YdaH and MtrF, thus hinting at convergence in structure and function. CitS and the related proteins are predicted to translocate their substrates by an elevator-like mechanism, in which a compact transport domain slides up and down through the membrane while the dimerization domain is stably anchored. Here we review the large body of available biochemical data on CitS in the light of the new crystal structure. We show that the biochemical data are fully consistent with the proposed elevator mechanism, but also demonstrate that the current structural data cannot explain how strict coupling of citrate and Na⁺ transport is achieved. We propose a testable model for the coupling mechanism.

Sequence motifs of myelin membrane proteins: towards the molecular basis of diseases

The shortest sequence of amino acids in protein containing functional and structural information is a "motif." To understand myelin protein functions, we intensively searched for motifs that can be found in myelin proteins. Some myelin proteins had several different motifs or repetition of the same motif. The most abundant motif found among myelin proteins was a myristoylation motif. Bovine MAG held 11 myristoylation motifs and human myelin basic protein held as many as eight such motifs. PMP22 had the fewest myristoylation motifs, which was only one; rat PMP22 contained no such motifs. Cholesterol recognition/interaction amino-acid consensus (CRAC) motif was not found in myelin basic protein. P2 protein of different species contained only one CRAC motif, except for P2 of horse, which had no such motifs. MAG, MOG, and P0 were very rich in CRAC, three to eight motifs per protein. The analysis of motifs in myelin proteins is expected to provide structural insight and refinement of predicted 3D models for which structures are as yet unknown. Analysis of motifs in mutant proteins associated with neurological diseases uncovered that some motifs disappeared in P0 with mutation found in neurological diseases. There are 2,500 motifs deposited in a databank, but 21 were found in myelin proteins, which is only 1% of the total known motifs. There was great variability in the number of motifs among proteins from different species. The appearance or disappearance of protein motifs after gaining point mutation in the protein related to neurological diseases was very interesting.

Projection structure of the secondary citrate/sodium symporter CitS at 6 Å resolution by electron crystallography

CitS from Klebsiella pneumoniae acts as a secondary symporter of citrate and sodium ions across the inner membrane of the host. The protein is the best characterized member of the 2-hydroxycarboxylate transporter family, while no experimental structural information at sub-nanometer resolution is available on this class of membrane proteins. Here, we applied electron crystallography to two-dimensional crystals of CitS. Carbon-film-adsorbed tubular two-dimensional crystals were studied by cryo-electron microscopy, producing the 6-Å-resolution projection structure of the membrane-embedded protein. In the p22(1)2(1)-symmetrized projection map, the predicted dimeric structure is clearly visible. Each monomeric unit can tentatively be interpreted as being composed of 11 transmembrane α-helices. In projection, CitS shows a high degree of structural similarity to NhaP1, the Na(+)/H(+) antiporter of Methanococcus jannaschii. We discuss possible locations for the dimer interface and models for the helical arrangements and domain organizations of the symporter based on existing models.

Turnover and accessibility of a reentrant loop of the Na+-glutamate transporter GltS are modulated by the central cytoplasmic loop

GltS of Escherichia coli is a secondary transporter that catalyzes Na+-glutamate symport. The structural model of GltS shows two homologous domains with inverted membrane topology that are connected by a central loop that resides in the cytoplasm. Each domain contains a reentrant loop structure. Accessibility of the Cys residues in two GltS mutants in which Pro351 and Asn356 in the reentrant loop in the C-terminal domain were replaced by Cys is demonstrated to be sensitive to the catalytic state supporting a role for the reentrant loops in catalysis. Saturating concentrations of the substrate L-glutamate protected both mutants against inactivation by thiol reagents, while the presence of the co-ion Na+ stimulated the inactivation of both mutants. Insertion of the 10 kDa biotin acceptor domain (BAD) of oxaloacetate decarboxylase of Klebsiella pneumoniae in the central cytoplasmic loop blocked the access pathway from the periplasmic side of the membrane to the cysteine residues in mutants P351C and N356C in the reentrant loop. Kinetically, insertion of BAD increased the maximal rate of uptake 2.7-fold while leaving the apparent affinity constants for L-glutamate and Na+ unaltered. The data suggests that insertion of BAD in the central loop results in conformational changes at the translocation site that lower the activation energy of the translocation step without affecting the access pathway from the periplasmic side for substrate and co-ions. It is concluded that changes in the central loop that connects the two domains may have a regulatory function on the activity of the transporter.

An extracellular loop of the mannose phosphotransferase system component IIC is responsible for specific targeting by class IIa bacteriocins

Class IIa bacteriocins target a phylogenetically defined subgroup of mannose-phosphotransferase systems (man-PTS) on sensitive cells. By the use of man-PTS genes of the sensitive Listeria monocytogenes (mpt) and the nonsensitive Lactococcus lactis (ptn) species to rationally design a series of man-PTS chimeras and site-directed mutations, we identified an extracellular loop of the membrane-located protein MptC that was responsible for specific target recognition by the class IIa bacteriocins.

Cross-linking of trans reentrant loops in the Na(+)-citrate transporter CitS of Klebsiella pneumoniae

The membrane topology model of the Na(+)-citrate transporter CitS of Klebsiella pneumoniae shows a core of two homologous domains with opposite orientation in the membrane and each containing a so-called reentrant loop. A split version of CitS was constructed to study domain interactions and proximity relationships of the putative reentrant loops. Split CitS retained 50% transport activity of the wild-type version in membrane vesicles. Unspecific cross-linking of the purified complex with glutaraldehyde revealed a tetrameric complex with two N and two C domains corresponding to dimeric CitS. The separately expressed domains were not detected in the membrane. Strong interaction between the two domains followed from successful purification of the whole complex by Ni(2+)-NTA chromatography when only one domain was His-tagged. The presence of citrate and/or the co-ion Na(+) during purification did not seem to affect the interaction significantly. Successful disulfide cross-linking was obtained between single cysteine residues introduced in the highly conserved GGNG sequence motif at the vertex of the reentrant loop in the N domain and either of two endogenous cysteine residues at the base of the reentrant loop in the C domain. The disulfide bond was formed within one subunit in the dimer. A model is proposed in which the reentrant loops in the N and C domains are overlapping at the domain interface in the 3D structure where they form (part of) the translocation pathway for substrate and co-ions.

Rapid screening of membrane topology of secondary transport proteins

Limited experimental data may be very useful to discriminate between membrane topology models of membrane proteins derived from different methods. A membrane topology screening method is proposed by which the cellular disposition of three positions in a membrane protein are determined, the N- and the C-termini and a position in the middle of the protein. The method involves amplification of the encoding genes or gene fragments by PCR, rapid cloning in dedicated vectors by ligation independent cloning, and determination of the cellular disposition of the three sites using conventional techniques. The N-terminus was determined by labeling with a fluorescent probe, the central position and the C-terminus by the reporter fusion technique using alkaline phosphatase (PhoA) and green fluorescence protein (GFP) as reporters. The method was evaluated using 16 transporter proteins of known function from four different structural classes. For 13 proteins a complete set of three localizations was obtained. The experimental data was used to discriminate between membrane topology models predicted by TMHMM, a widely used predictor using the amino acid sequence as input and by MemGen that uses hydropathy profile alignment and known 3D structures or existing models. It follows that in those cases where the models from the two methods were similar, the models were consistent with the experimental data. In those cases where the models differed, the MemGen model agreed with the experimental data. Three more recent predictors, MEMSAT3, OCTOPUS and TOPCONS showed a significantly higher consistency with the experimental data than observed with TMHMM.