[Show abstract][Hide abstract] ABSTRACT: Bacterial conjugation is one of the main mechanisms for horizontal gene transfer. It constitutes a key element in the dissemination of antibiotic resistance and virulence genes to human pathogenic bacteria. DNA transfer is mediated by a membrane-associated macromolecular machinery called Type IV secretion system (T4SS). T4SSs are involved not only in bacterial conjugation but also in the transport of virulence factors by pathogenic bacteria. Thus, the search for specific inhibitors of different T4SS components opens a novel approach to restrict plasmid dissemination. This review highlights recent biochemical and structural findings that shed new light on the molecular mechanisms of DNA and protein transport by T4SS. Based on these data, a model for pilus biogenesis and substrate transfer in conjugative systems is proposed. This model provides a renewed view of the mechanism that might help to envisage new strategies to curb the threating expansion of antibiotic resistance.This article is protected by copyright. All rights reserved.
[Show abstract][Hide abstract] ABSTRACT: Pilus biogenesis and substrate transport by type IV secretion systems require energy, which is provided by three molecular
motors localized at the base of the secretion channel. One of these motors, VirB11, belongs to the superfamily of traffic
ATPases, which includes members of the type II secretion system and the type IV pilus and archaeal flagellar assembly apparatus.
Here, we report the functional interactions between TrwD, the VirB11 homolog of the conjugative plasmid R388, and TrwK and
TrwB, the motors involved in pilus biogenesis and DNA transport, respectively. Although these interactions remained standing
upon replacement of the traffic ATPase by a homolog from a phylogenetically related conjugative system, namely, TraG of plasmid
pKM101, this homolog could not replace the TrwD function for DNA transfer. This result suggests that VirB11 works as a switch
between pilus biogenesis and DNA transport and reinforces a mechanistic model in which VirB11 proteins act as traffic ATPases
by regulating both events in type IV secretion systems.
Journal of bacteriology 07/2013; 195(18). DOI:10.1128/JB.00437-13 · 2.81 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: VirB4 proteins are ATPases essential for pilus biogenesis and protein transport in Type IV secretion systems. These proteins contain a motor domain which shares structural similarities with the motor domains of DNA translocases, such as the VirD4/TrwB conjugative coupling proteins and the chromosome segregation pump FtsK. Here, we report the three dimensional structure of full length TrwK, the VirB4 homologue in the conjugative plasmid R388, determined by single particle electron microscopy. The structure consists of a hexameric double ring with a barrel-shaped structure. Docking the atomic coordinates of the crystal structures of TrwB and FtsK into the EM map revealed a better fit for FtsK. Interestingly, we have found that, likewise TrwB, TrwK is able to bind DNA, with higher affinity for G4 quadruplex structures than for single stranded DNA. Furthermore, TrwK exerts a dominant negative effect on the ATPase activity of TrwB, which reflects an interaction between the two proteins. Our studies provide new insights into the structure-function relationship and the evolution of these DNA and protein translocases.
Biophysical aspects on T4SS. Biophysics Unit of Basque Country University (UPV) . Biophysics Unit of Basque Country University (UPV). Biophysics Unit of Basque Country University (UPV) . Biophysics Unit of Basque Country University (UPV) . Biophysics Unit, Bilbao; 09/2012
[Show abstract][Hide abstract] ABSTRACT: TrwD, the VirB11 homologue in conjugative plasmid R388, is a member of the large secretion ATPase superfamily, which includes ATPases from bacterial type II and type IV secretion systems, type IV pilus, and archaeal flagellae assembly. Based on structural studies of the VirB11 homologues in Helicobacter pylori and Brucella suis and the archaeal type II secretion ATPase GspE, a unified mechanism for the secretion ATPase superfamily has been proposed. Here, we have found that the ATP turnover of TrwD is down-regulated by physiological concentrations of magnesium. This regulation is exerted by increasing the affinity for ADP, hence delaying product release. Circular dichroism and limited proteolysis analysis indicate that magnesium induces conformational changes in the protein that promote a more rigid, but less active, form of the enzyme. The results shown here provide new insights into the catalytic mechanism of the secretion ATPase superfamily.
[Show abstract][Hide abstract] ABSTRACT: Nature has endowed cells with powerful nanomotors to accomplish intricate mechanical tasks, such as the macromolecular transport across membranes occurring in cell division, bacterial conjugation, and in a wide variety of secretion systems. These biological motors couple the chemical energy provided by ATP hydrolysis to the mechanical work needed to transport DNA and/or protein effectors. Here, we review what is known about the molecular mechanisms of these membrane-associated machines. Sequence and structural comparison between these ATPases reveal that they share a similar motor domain, suggesting a common evolutionary ancestor. Learning how these machines operate will lead the design of nanotechnology devices with unique applications in medicine and engineering.
Current Opinion in Biotechnology 12/2011; 23(4):537-44. DOI:10.1016/j.copbio.2011.11.031 · 7.12 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Type IV secretion systems (T4SS) mediate the transfer of DNA and protein substrates to target cells. TrwK, encoded by the conjugative plasmid R388, is a member of the VirB4 family, comprising the largest and most conserved proteins of T4SS. In a previous work we demonstrated that TrwK is able to hydrolyze ATP. Here, based on the structural homology of VirB4 proteins with the DNA-pumping ATPase TrwB coupling protein, we generated a series of variants of TrwK where fragments of the C-terminal domain were sequentially truncated. Surprisingly, the in vitro ATPase activity of these TrwK variants was much higher than that of the wild-type enzyme. Moreover, addition of a synthetic peptide containing the amino acid residues comprising this C-terminal region resulted in the specific inhibition of the TrwK variants lacking such domain. These results indicate that the C-terminal end of TrwK plays an important regulatory role in the functioning of the T4SS.
[Show abstract][Hide abstract] ABSTRACT: TrwB is a DNA-dependent ATPase involved in DNA transport during bacterial conjugation. The protein presents structural similarity to hexameric molecular motors such as F(1)-ATPase, FtsK, or ring helicases, suggesting that TrwB also operates as a motor, using energy released from ATP hydrolysis to pump single-stranded DNA through its central channel. In this work, we have carried out an extensive analysis with various DNA substrates to determine the preferred substrate for TrwB. Oligonucleotides with G-rich sequences forming G4 DNA structures were the optimal substrates for TrwB ATPase activity. The protein bound with 100-fold higher affinity to G4 DNA than to single-stranded DNA of the same sequence. Moreover, TrwB formed oligomeric protein complexes only with oligonucleotides presenting such a G-quadruplex DNA structure, consistent with stoichiometry of six TrwB monomers to G4 DNA, as demonstrated by gel filtration chromatography and analytical ultracentrifugation experiments. A protein-DNA complex was also formed with unstructured oligonucleotides, but the molecular mass corresponded to one monomer protein bound to one oligonucleotide molecule. Sequences capable of forming G-quadruplex structures are widespread through genomes and are thought to play a biological function in transcriptional regulation. They form stable structures that can obstruct DNA replication, requiring the action of specific helicases to resolve them. Nevertheless, TrwB displayed no G4 DNA unwinding activity. These observations are discussed in terms of a possible role for TrwB in recognizing G-quadruplex structures as loading sites on the DNA.
[Show abstract][Hide abstract] ABSTRACT: Selective substrate uptake controls initiation of macromolecular secretion by type IV secretion systems in gram-negative bacteria. Type IV coupling proteins (T4CPs) are essential, but the molecular mechanisms governing substrate entry to the translocation pathway remain obscure. We report a biochemical approach to reconstitute a regulatory interface between the plasmid R1 T4CP and the nucleoprotein relaxosome dedicated to the initiation stage of plasmid DNA processing and substrate presentation. The predicted cytosolic domain of T4CP TraD was purified in a predominantly monomeric form, and potential regulatory effects of this protein on catalytic activities exhibited by the relaxosome during transfer initiation were analyzed in vitro. TraDDeltaN130 stimulated the TraI DNA transesterase activity apparently via interactions on both the protein and the DNA levels. TraM, a protein interaction partner of TraD, also increased DNA transesterase activity in vitro. The mechanism may involve altered DNA conformation as TraM induced underwinding of oriT plasmid DNA in vivo (DeltaL(k) = -4). Permanganate mapping of the positions of duplex melting due to relaxosome assembly with TraDDeltaN130 on supercoiled DNA in vitro confirmed localized unwinding at nic but ruled out formation of an open complex compatible with initiation of the TraI helicase activity. These data link relaxosome regulation to the T4CP and support the model that a committed step in the initiation of DNA export requires activation of TraI helicase loading or catalysis.
Journal of bacteriology 09/2009; 191(22):6877-87. DOI:10.1128/JB.00918-09 · 2.81 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Conjugative systems contain an essential integral membrane protein involved in DNA transport called the Type IV coupling protein (T4CP). The T4CP of conjugative plasmid R388 is TrwB, a DNA-dependent ATPase. Biochemical and structural data suggest that TrwB uses energy released from ATP hydrolysis to pump DNA through its central channel by a mechanism similar to that used by F1-ATPase or ring helicases. For DNA transport, TrwB couples the relaxosome (a DNA-protein complex) to the secretion channel. In this work we show that TrwA, a tetrameric oriT DNA-binding protein and a component of the R388 relaxosome, stimulates TrwBDeltaN70 ATPase activity, revealing a specific interaction between the two proteins. This interaction occurs via the TrwA C-terminal domain. A 68-kDa complex between TrwBDeltaN70 and TrwA C-terminal domain was observed by gel filtration chromatography, consistent with a 1:1 stoichiometry. Additionally, electron microscopy revealed the formation of oligomeric TrwB complexes in the presence, but not in the absence, of TrwA protein. TrwBDeltaN70 ATPase activity in the presence of TrwA was further enhanced by DNA. Interestingly, maximal ATPase rates were achieved with TrwA and different types of dsDNA substrates. This is consistent with a role of TrwA in facilitating the interaction between TrwB and DNA. Our findings provide a new insight into the mechanism by which TrwB recruits the relaxosome for DNA transport. The process resembles the mechanism used by other DNA-dependent molecular motors, such as the RuvA/RuvB system, to be targeted to the DNA followed by hexamer assembly.
[Show abstract][Hide abstract] ABSTRACT: The mechanism by which TrwB acts as a DNA transporter in bacterial conjugation is analyzed. Based on a parallelism between TrwB and F(1)-ATPase, TrwB would use the energy derived from ATP hydrolysis to pump DNA through its central channel, in a manner similar to that used by F(1)-ATPase to produce a rotary movement of the central gamma-subunit.
Research in Microbiology 06/2006; 157(4):299-305. DOI:10.1016/j.resmic.2005.12.002 · 2.71 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Bacterial conjugation is an example of macromolecular trafficking between cells, based on the translocation of single-stranded DNA across membranes through a type IV secretion system. TrwBDeltaN70 is the soluble domain of TrwB, an essential integral membrane protein that couples the relaxosome (a nucleoprotein complex) to the DNA transport apparatus in plasmid R388 conjugation. TrwBDeltaN70 crystallographic structure revealed a hexamer with six equivalent subunits and a central channel. In this work, we characterize a DNA-dependent ATPase activity for TrwBDeltaN70. The protein displays positive cooperativity for ATP hydrolysis, with at least three catalytic sites involved. The activity is sensitive to pH and salt concentration, being more active at low pH values. The effective oligonucleotide size required for activation of the ATPase function is between 40 and 45 nucleotides, and the same length is required for the formation of high-molecular-weight TrwBDeltaN70-DNA complexes, as observed by gel filtration chromatography. A mutation in a tryptophan residue (W216A), placed in the central pore formed by the hexameric structure, resulted in a protein that did not hydrolyze ATP. In addition, it exerted a dominant negative effect, both on R388 conjugation frequency and ATP hydrolysis, underscoring the multimeric state of the protein. ATP hydrolysis was not coupled to a DNA unwinding activity under the tested conditions, which included forked DNA substrates. These results, together with TrwB structural similarity to F1-ATPase, lead us to propose a mechanism for TrwB as a DNA-translocating motor.
Proceedings of the National Academy of Sciences 07/2005; 102(23):8156-61. DOI:10.1073/pnas.0503402102 · 9.67 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: In mitochondria, the hydrolytic activity of ATP synthase is prevented by an inhibitor protein, IF1. The active bovine protein (84 amino acids) is an alpha-helical dimer with monomers associated via an antiparallel alpha-helical coiled coil composed of residues 49-81. The N-terminal inhibitory sequences in the active dimer bind to two F1-ATPases in the presence of ATP. In the crystal structure of the F1-IF1 complex at 2.8 A resolution, residues 1-37 of IF1 bind in the alpha(DP)-beta(DP) interface of F1-ATPase, and also contact the central gamma subunit. The inhibitor opens the catalytic interface between the alpha(DP) and beta(DP) subunits relative to previous structures. The presence of ATP in the catalytic site of the beta(DP) subunit implies that the inhibited state represents a pre-hydrolysis step on the catalytic pathway of the enzyme.
[Show abstract][Hide abstract] ABSTRACT: The effect of high-density lipoprotein (HDL) in protecting against atherosclerosis is usually attributed to its role in 'reverse cholesterol transport'. In this process, HDL particles mediate the efflux and the transport of cholesterol from peripheral cells to the liver for further metabolism and bile excretion. Thus, cell-surface receptors for HDL on hepatocytes are chief partners in the regulation of cholesterol homeostasis. A high-affinity HDL receptor for apolipoprotein A-I (apoA-I) was previously identified on the surface of hepatocytes. Here we show that this receptor is identical to the beta-chain of ATP synthase, a principal protein complex of the mitochondrial inner membrane. Different experimental approaches confirm this ectopic localization of components of the ATP synthase complex and the presence of ATP hydrolase activity at the hepatocyte cell surface. Receptor stimulation by apoA-I triggers the endocytosis of holo-HDL particles (protein plus lipid) by a mechanism that depends strictly on the generation of ADP. We confirm this effect on endocytosis in perfused rat liver ex vivo by using a specific inhibitor of ATP synthase. Thus, membrane-bound ATP synthase has a previously unsuspected role in modulating the concentrations of extracellular ADP and is regulated by a principal plasma apolipoprotein.
[Show abstract][Hide abstract] ABSTRACT: In Saccharomyces cerevisiae, at least three proteins (IF(1), STF(1), and STF(2)) appear to be involved in the regulation of ATP synthase. Both IF(1) and STF(1) inhibit F(1), whereas the proposed function for STF(2) is to facilitate the binding of IF(1) and STF(1) to F(1). The oligomerization properties of yeast IF(1) and STF(1) have been investigated by sedimentation equilibrium analytical ultracentrifugation and by covalent cross-linking. Both techniques confirm that IF(1) and STF(1) oligomerize in opposite directions in relation to pH, suggesting that both proteins might regulate yeast F(1)F(0)-ATPase under different conditions. Their effects on bovine F-ATPases are also described. Whereas bovine IF(1) inhibits yeast F(1)-ATPase even better than yeast IF(1) or STF(1), the capability of yeast IF(1) to inhibit the bovine enzyme is very low and decreases with time. Such an effect is also observed in the study of the homologous inhibition of yeast F(1)-ATPase. Yeast inhibitors are not as effective as their bovine counterpart, and the complex seems to dissociate gradually.
[Show abstract][Hide abstract] ABSTRACT: In mitochondria, the hydrolytic activity of ATP synthase is regulated by an inhibitor protein, IF(1). Its binding to ATP synthase depends on pH, and below neutrality, IF(1) is dimeric and forms a stable complex with the enzyme. At higher pH values, IF(1) forms tetramers and is inactive. In the 2.2 A structure of the bovine IF(1) described here, the four monomers in the asymmetric unit are arranged as a dimer of dimers. Monomers form dimers via an antiparallel alpha-helical coiled coil in the C-terminal region. Dimers are associated into oligomers and form long fibres in the crystal lattice, via coiled-coil interactions in the N-terminal and inhibitory regions (residues 14-47). Therefore, tetramer formation masks the inhibitory region, preventing IF(1) binding to ATP synthase.
The EMBO Journal 12/2001; 20(24):6990-6996. DOI:10.1093/emboj/20.24.6990 · 10.43 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: The transfer of DNA across membranes and between cells is a central
biological process; however, its molecular mechanism remains unknown. In
prokaryotes, trans-membrane passage by bacterial conjugation, is the
main route for horizontal gene transfer. It is the means for rapid
acquisition of new genetic information, including antibiotic resistance
by pathogens. Trans-kingdom gene transfer from bacteria to plants or
fungi and even bacterial sporulation are special cases of conjugation.
An integral membrane DNA-binding protein, called TrwB in the Escherichia
coli R388 conjugative system, is essential for the conjugation process.
This large multimeric protein is responsible for recruiting the
relaxosome DNA-protein complex, and participates in the transfer of a
single DNA strand during cell mating. Here we report the
three-dimensional structure of a soluble variant of TrwB. The molecule
consists of two domains: a nucleotide-binding domain of α/β
topology, reminiscent of RecA and DNA ring helicases, and an all-α
domain. Six equivalent protein monomers associate to form an almost
spherical quaternary structure that is strikingly similar to
F1-ATPase. A central channel, 20Å in width, traverses