CORD-19-Sentences  

CORD-19:096d93f37dc46f318615812c537eaf4a14dc673e JSONTXT 7 Projects

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Id Subject Object Predicate Lexical cue
TextSentencer_T1 0-29 Sentence denotes Competing interests statement
TextSentencer_T2 31-63 Sentence denotes between two cell membranes (FIG.
TextSentencer_T3 64-68 Sentence denotes 1) .
TextSentencer_T4 69-211 Sentence denotes Also, nonenveloped viruses follow a separate pathway of cell entry 5, 6 , which seems to be mediated by proteins that have a similar topology.
TextSentencer_T5 212-409 Sentence denotes Compared with the above-mentioned viral and eukaryotic fusion events, relatively little is known about the molecular mechanisms that allow bacteria access to the internal milieu of host cells (FIG.
TextSentencer_T6 410-414 Sentence denotes 1) .
TextSentencer_T7 415-601 Sentence denotes What is known is that this process is mediated by a family of surface proteins that are known as bacterial INVASINS and, as in viral entry, bacterial entry requires actin polymerization.
TextSentencer_T8 602-822 Sentence denotes Following host cell-receptor binding, invasins trigger the phosphorylation and dephosphorylation of cytoskeleton effector molecules and scaffolding proteins, which results in bacterial internalization 6-10 (endocytosis).
TextSentencer_T9 823-911 Sentence denotes However, it is not known whether invasins play a further part in bacterial pathogenesis.
TextSentencer_T10 912-1094 Sentence denotes Evidence from this report indicates that a family of bacterial cellentry proteins shares the modular organization of SNARE heterotetramers and viral homotrimeric spike proteins (FIG.
TextSentencer_T11 1095-1099 Sentence denotes 2) .
TextSentencer_T12 1100-1293 Sentence denotes It is intriguing to speculate that, because of their conserved modular architecture -which is defined by a membrane anchor, a central COILED-COIL motif and a receptor-binding domain (RBD) (FIG.
TextSentencer_T13 1294-1393 Sentence denotes 2a) -viral fusion proteins, bacterial invasins and SNAREs might share similar mechanisms of action.
TextSentencer_T14 1394-1616 Sentence denotes The absence of amino-acid homology coupled to the analogous distribution of domains indicates a common mechanism that might add selective advantages to the pathogen, which would ensure survival in a particular environment.
TextSentencer_T15 1617-1769 Sentence denotes Furthermore, this indicates that different organisms might have evolved common solutions when challenged with the task of penetrating cellular barriers.
TextSentencer_T16 1770-1797 Sentence denotes Vesicles -the SNARE family.
TextSentencer_T17 1798-2053 Sentence denotes In 1992, a seminal discovery showed that proteolytic cleavage of a membrane fusion protein, known as VAMP1, by the tetanus toxin was sufficient to inhibit the secretion of neurotransmitters from synaptic junctions and cause the deadly tetanus disease 11 .
TextSentencer_T18 2054-2308 Sentence denotes This finding led to the understanding that intracellular Abstract | Molecular machines orchestrate the translocation and entry of pathogens through host cell membranes, in addition to the uptake and release of molecules during endocytosis and exocytosis.
TextSentencer_T19 2309-2562 Sentence denotes Viral cell entry requires a family of glycoproteins, and the structural organization and function of these viral glycoproteins are similar to the SNARE proteins, which are known to be involved in intracellular vesicle fusion, endocytosis and exocytosis.
TextSentencer_T20 2563-2865 Sentence denotes Here, we propose that a family of bacterial membrane proteins that are responsible for cell-mediated adherence and entry resembles the structural architecture of both viral fusion proteins and eukaryotic SNAREs and might therefore share similar, but distinct, mechanisms of cell membrane translocation.
TextSentencer_T21 2866-3132 Sentence denotes Furthermore, we propose that the recurrence of these molecular machines across species indicates that these architectural motifs were evolutionarily selected because they provided the best solution to ensure the survival of pathogens within a particular environment.
TextSentencer_T22 3133-3363 Sentence denotes The eukaryotic plasma membrane has evolved to control and regulate the entry of fluids, solutes and particles into cells from the extracellular environment and to regulate the export of intracellular components stored in vesicles.
TextSentencer_T23 3364-3411 Sentence denotes This is achieved by endocytosis and exocytosis.
TextSentencer_T24 3412-3575 Sentence denotes In parallel, microorganisms such as viruses and bacteria have developed mechanisms to enter host cells to facilitate their replication, transport and transmission.
TextSentencer_T25 3576-3808 Sentence denotes One of the recent breakthroughs in cell biology has been the understanding that molecular machines that share similarities both in structural domains and functional mechanisms mediate both viral entry and cellular exocytosis events.
TextSentencer_T26 3809-3890 Sentence denotes The fusion between cell membranes during vesicle trafficking and exocytosis (FIG.
TextSentencer_T27 3891-4011 Sentence denotes 1) is mediated by a conserved set of tetrameric proteins, collectively known as SNARES [1] [2] [3] [4] (see Glossary) .
TextSentencer_T28 4012-4294 Sentence denotes Similarly, the entry of enveloped viruses into host cells is mediated by a family of glycoproteins that usually fold as homotrimers and that mediate the fusion complex assembles through the hydrophobic and ionic core-packing interactions that are formed between vSNAREs and tSNAREs.
TextSentencer_T29 4295-4519 Sentence denotes The free energy that is derived from the formation of the four-helix bundle and a subsequent conformational change promotes tethering of the two opposing membranes to mediate subsequent fusion events [2] [3] [4] 12, 14, 15 .
TextSentencer_T30 4520-4617 Sentence denotes Such fusion events mediate either exocytosis of secretory vesicles or endosomal trafficking (FIG.
TextSentencer_T31 4618-4897 Sentence denotes 1) ; and they involve additional factors, such as the exocyst multi-subunit protein docking complex, microtubules and the recruitment of tethering proteins through Rab GTPases (such as Rab3A) 15, 16 that specify the fusion of transport vesicles with a particular target membrane.
TextSentencer_T32 4898-5084 Sentence denotes Conceptually, all enveloped viruses require a similar membrane fusion event to deliver their genomes into the host cell cytoplasm for the replication and transmission of new virions 17 .
TextSentencer_T33 5085-5291 Sentence denotes The entry of many enveloped viruses is mediated by glycoproteins (called 'spikes'), which are expressed as trimers on the external surface of the viral particle, where they form a halo-like appearance (FIG.
TextSentencer_T34 5292-5299 Sentence denotes 2c,d) .
TextSentencer_T35 5300-5710 Sentence denotes These viral fusion proteins have several common features: first, the presence of a generally hydrophobic FUSION PEPTIDE that participates in the first phase of membrane fusion; second, an energetically metastable region that is characterized by coiled-coil HEPTAD REPEATS (HR1 and HR2), which form higher order oligomers on the viral membrane; and last, all possess a C-terminal membrane anchor domain 17 (FIG.
TextSentencer_T36 5711-5718 Sentence denotes 2c,d) .
TextSentencer_T37 5719-5890 Sentence denotes On binding with a receptor, many viral fusion proteins undergo a conformational change that is required to expose the fusion peptide, which anchors the host cell membrane.
TextSentencer_T38 5891-6130 Sentence denotes Although fusion peptides of different viruses are variable in structure, hydrophobic residues are important for coiled-coil formation, whereas the ability of these peptides to form trimers is crucial for fusogenic activity [18] [19] [20] .
TextSentencer_T39 6131-6395 Sentence denotes It has been hypothesized that the energy released from a conformational change is important to expose and deliver the fusion peptide to the target membrane, successively driving the formation of the fusion pore and eventually joining the membranes 14, 19, 21, 22 .
TextSentencer_T40 6396-6608 Sentence denotes Viral fusion proteins are classified as class I and class II fusion proteins according to the location of the fusion peptide and the orientation of the glycoprotein relative to the viral envelope [22] [23] [24] .
TextSentencer_T41 6609-7035 Sentence denotes Class I fusion proteins are expressed by human pathogens such as the influenza virus and HIV and form trimeric 'spikes' in their native metastable conformation (vesicle SNARE) from the vesicle membrane 12, 13 , and the crystal structures of short coiled-coil fragments indicate that this interaction results in the formation of a supercoil complex, which consists of a heterotetramer of four parallel α-helices 2, 14, 15 (FIG.
TextSentencer_T42 7036-7041 Sentence denotes 2b) .
TextSentencer_T43 7042-7120 Sentence denotes This fusion during exocytosis was carried out by specialized proteins, SNAREs.
TextSentencer_T44 7121-7202 Sentence denotes The SNARE superfamily comprises more than 35 eukaryotic membrane fusion proteins.
TextSentencer_T45 7203-7332 Sentence denotes To mediate fusion, three SNAREs from the target membrane (tSNAREs) recognize one vSNARE haemagglutinin is a pH-dependent process.
TextSentencer_T46 7333-7427 Sentence denotes Haemagglutinin is a trimeric glycoprotein that projects 135Å from the target membrane 26 (FIG.
TextSentencer_T47 7428-7433 Sentence denotes 2c) .
TextSentencer_T48 7434-7525 Sentence denotes Each monomer is composed of a globular receptor-binding subunit HA 1 (shown in blue in FIG.
TextSentencer_T49 7526-7616 Sentence denotes 2) , and a triple-stranded coiled-coil fibrous region, known as HA 2 (shown in red in FIG.
TextSentencer_T50 7617-7621 Sentence denotes 2) .
TextSentencer_T51 7622-7807 Sentence denotes Data from the crystal structure of haemagglutinin before and after the pH-induced conformational change allowed an understanding of the mechanism of viral fusion with the host cell 27 .
TextSentencer_T52 7808-7892 Sentence denotes In this multistep process, haemagglutinin binds surface-exposed cell receptors (FIG.
TextSentencer_T53 7893-7897 Sentence denotes 1) .
TextSentencer_T54 7898-8126 Sentence denotes The virus is then internalized, and the subsequent acidification of the endosome causes a conformational change of haemagglutinin (irreversible in most cases), and triggers the fusion of the viral and endosomal membrane 28, 29 .
TextSentencer_T55 8127-8428 Sentence denotes Similar to haemagglutinin of the influenza virus, class I viral fusion proteins from HIV, Visna virus, and SARS-CoV are characterized by a central domain, which during fusion, adopts a trimer of 'hairpins' folds, which leads to the assembly of a six-helix, coiled-coil bundle 25, [30] [31] [32] [33] .
TextSentencer_T56 8429-8503 Sentence denotes However, in these cases, the fusion event is not dependent on a pH change.
TextSentencer_T57 8504-8838 Sentence denotes Specifically, during cell entry of HIV, insertion of the HIV envelope protein (Env) fusion peptide into the host cell membrane is followed by the formation of a complete coiled-coil structure, which involves the folding of the HR1 heptad repeat of the stalk over the second heptad repeat HR2, and assembly of the six-helix bundle 21 .
TextSentencer_T58 8839-9000 Sentence denotes The free energy that is released by this conformational change is required to draw the viral and host membranes into close proximity until fusion occurs 30 (FIG.
TextSentencer_T59 9001-9005 Sentence denotes 1) .
TextSentencer_T60 9006-9151 Sentence denotes The formation of this coiledcoil structure is essential for the fusogenic function of Env and for the infection of CD4 + T cells [34] [35] [36] .
TextSentencer_T61 9152-9328 Sentence denotes Inhibiting its formation by blocking the HR1 domain -for example, with a synthetic peptide such as Enfuvirtide, which mimics the function of HR2 -impedes the fusion of HIV 37 .
TextSentencer_T62 9329-9636 Sentence denotes By contrast, class II fusion protein heterodimers contain an internal fusion peptide and, when exposed to low pH, these fusion proteins reversibly dissociate from their partner to form irreversible homotrimers, which in turn mediate membrane fusion by a mechanism similar to the one described above 38, 39 .
TextSentencer_T63 9637-9834 Sentence denotes Class II fusion proteins are found in flaviviruses such as dengue virus 29 , hepatitis C virus (HCV), tick-borne encephalitis (TBE) virus 39 , and alphaviruses such as the Semliki Forest virus 40 .
TextSentencer_T64 9835-9996 Sentence denotes Non-enveloped viruses, such as picornaviruses and rotaviruses, lack a lipid bilayer membrane and therefore cannot achieve cell entry through membrane fusion 41 .
TextSentencer_T65 9997-10050 Sentence denotes Despite at the surface of the infectious virions 25 .
TextSentencer_T66 10051-10296 Sentence denotes Their post-fusion conformation is a hairpin-like structure in which both the fusion peptide (proximal to the N-terminus) and the membrane anchor (distal to the N-terminus) are juxtaposed at the same end of a stable protein 'rod' or 'spike' (FIG.
TextSentencer_T67 10297-10301 Sentence denotes 1) .
TextSentencer_T68 10302-10397 Sentence denotes The influenza virus haemagglutinin (HA) is considered the prototype of class I fusion proteins.
TextSentencer_T69 10398-10526 Sentence denotes The fusion that is mediated by b | Partial three-dimensional structure of the coiled-coil domains of the synaptic SNARE complex.
TextSentencer_T70 10527-10610 Sentence denotes Synaptobrevin 2 (also known as VAMP2) (yellow) is anchored to the vesicle membrane.
TextSentencer_T71 10611-10680 Sentence denotes Syntaxin (pink) and SNAP25 (red) are anchored to the target membrane.
TextSentencer_T72 10681-10953 Sentence denotes These proteins are anchored to the cytoplasmic membrane by a hydrophobic α-helical C-terminal domain, which allows the protein to extend 120Å from the cell membrane. c | Structural representation of the influenza haemagglutinin (HA) trimer with the fusion peptide (green).
TextSentencer_T73 10954-11005 Sentence denotes The stalk is in its metastable pre-fusogenic state.
TextSentencer_T74 11006-11279 Sentence denotes The globular receptor-binding subunit HA 1 is shown in blue, and the triple-stranded, coiled-coil fibrous region, known as HA 2 , is shown in red. d | The HIV envelope protein (Env) is composed of two non-covalently associated trimeric gp120 (red) and gp41 (blue) subunits.
TextSentencer_T75 11280-11322 Sentence denotes Here, gp120 is artificially fused to gp41.
TextSentencer_T76 11323-11390 Sentence denotes The fusion peptide, which is located in gp41, is depicted in green.
TextSentencer_T77 11391-11593 Sentence denotes In their monomeric form, both fusion proteins -haemagglutinin and Env -span the viral envelope with a single transmembrane α-helix near the C-terminus. e | Structural model of the trimeric Yersinia spp.
TextSentencer_T78 11594-11675 Sentence denotes YadA molecule anchored to the bacterial outer membrane through a β-barrel (blue).
TextSentencer_T79 11676-11809 Sentence denotes The anchor domain is represented by a porin-like outer membrane protein. thereby allowing the virion to penetrate into the cytoplasm.
TextSentencer_T80 11810-11915 Sentence denotes This mechanism of cell entry, although not well understood, recalls that described for enveloped viruses.
TextSentencer_T81 11916-12116 Sentence denotes Also, such a membrane-fusion-independent method of host cell penetration might represent a possible link between the cell entry mechanisms and molecular machines that are used by viruses and bacteria.
TextSentencer_T82 12117-12244 Sentence denotes In addition to the fusion of enveloped viruses with their host, membrane-fusion events in prokaryotes have also been described.
TextSentencer_T83 12245-12478 Sentence denotes In vitro fragments cluster to form a homotrimer that is composed of three globular domains that are folded over an α-helical triple coiled-coil stalk, which is reminiscent of the structure of spike proteins from enveloped viruses 5 .
TextSentencer_T84 12479-12746 Sentence denotes A possible mechanism of cell entry is proposed in which the interaction of the rotavirus membrane penetration protein with the host cell receptor promotes a conformational change that leads to the formation of the observed trimer and to the release of the VP8 domain.
TextSentencer_T85 12747-12973 Sentence denotes The hydrophobic fusion domain of VP5 is exposed and might be used to breach or permeabilize the host cell membrane, years of study, the mechanism that allows this class of viruses to cross a membrane remains poorly understood.
TextSentencer_T86 12974-13108 Sentence denotes However, it seems that these viruses might enter cells using proteins that have a similar topology to those used by enveloped viruses.
TextSentencer_T87 13109-13272 Sentence denotes Recently, work by Dormitzer and colleagues reported the structural characterization of a domain of the membrane penetration protein -the VP4 spike of rotavirus 5 .
TextSentencer_T88 13273-13365 Sentence denotes VP4 haemagglutinin is a dimer that is present on the external surface of the virion 42, 43 .
TextSentencer_T89 13366-13471 Sentence denotes Following trypsin cleavage of the VP4 spike, two virion-associated fragments, VP8 and VP5, are generated.
TextSentencer_T90 13472-13697 Sentence denotes The VP5 left-handed coiled-coil segments, which are implicated in the formation of higher-order oligomers; and an N-terminal globular head region that is involved in binding to host cells and the extracellular matrix 63 (FIG.
TextSentencer_T91 13698-13705 Sentence denotes 2a,e) .
TextSentencer_T92 13706-13793 Sentence denotes Recently, the crystal structure of the collagen-binding domain of YadA was solved (FIG.
TextSentencer_T93 13794-13924 Sentence denotes 2e) , revealing a novel, nine-coiled, left-handed parallel β-roll 64 , a structure that is commonly found in fibrous proteins 65 .
TextSentencer_T94 13925-13933 Sentence denotes In FIG.
TextSentencer_T95 13934-14132 Sentence denotes 2e , the X-ray-determined structure of the YadA head domain has been arbitrarily fused to structural models of the stalk and membrane anchor regions, which have been derived from THREADING ANALYSES.
TextSentencer_T96 14133-14329 Sentence denotes Like YadA, NadA forms stable, highmolecular-weight oligomers on the surface of N. meningitidis 58 and, when expressed in E. coli, is exported to the outer membrane where it assembles into trimers.
TextSentencer_T97 14330-14430 Sentence denotes The trimeric conformation of NadA has been confirmed experimentally by light scattering analysis (S.
TextSentencer_T98 14431-14463 Sentence denotes Savino, personal communication).
TextSentencer_T99 14464-14704 Sentence denotes Detailed analysis of the NadA primary and secondary structure profiles, and comparison with coiled-coil regions of viral glycoproteins has allowed the prediction of the two putative heptad repeat domains HR1 and HR2 within the stalk region.
TextSentencer_T100 14705-14926 Sentence denotes In the absence of threedimensional data, the presence of a coiled-coil structure for NadA was partially confirmed by CIRCULAR DICHROISM (CD) SPECTRA ANALYSIS, which shows a prominent α-helical content for this protein (S.
TextSentencer_T101 14927-14959 Sentence denotes Savino, personal communication).
TextSentencer_T102 14960-15255 Sentence denotes Although it is not clear whether these predicted domains have a function, preliminary analysis shows that purified NadA undergoes temperature-and pH-inducible conformational changes that are visible in SDS-PAGE, indicative of a metastable structure similar to that of viral spikes and SNAREs (S.
TextSentencer_T103 15256-15288 Sentence denotes Savino, personal communication).
TextSentencer_T104 15289-15504 Sentence denotes Besides common structural features, the Oca family proteins and viral fusion proteins also share functional characteristics, such as binding to host cell structures and mediating immunological protection (TABLE 2) .
TextSentencer_T105 15505-15627 Sentence denotes It has been reported that, similar to InvA, YadA-promoted cell entry occurs through the interaction with β1-integrins 66 .
TextSentencer_T106 15628-15673 Sentence denotes Whereas the interaction between Yersinia spp.
TextSentencer_T107 15674-15883 Sentence denotes InvA and β1-integrins is direct 67 , YadA interaction with host cells is mediated indirectly by a bridging mechanism involving extracellular matrix components, such as collagen and fibronectin [68] [69] [70] .
TextSentencer_T108 15884-15949 Sentence denotes Several important reports have linked YadA to bacterial invasion.
TextSentencer_T109 15950-16348 Sentence denotes YadA is expressed in both Yersinia enterocolitica and Yersinia pseudotuberculosis, but not in Yersinia pestis 71 . assays coupled with transmission electron microscopy provide evidence that the segmented double-stranded RNA enveloped bacteriophage φ6 expresses a trimeric structure that is involved in the fusion with the outer membrane of its host, the plant pathogen Pseudomonas syringae 44, 45 .
TextSentencer_T110 16349-16602 Sentence denotes An additional lipid-containing, double-stranded DNA bacteriophage, PRD1, known to infect Gram-negative pathogens such as Escherichia coli, Salmonella spp. and Pseudomonas spp., has been proposed to fuse with the bacterial membrane on infection 46,47 (S.
TextSentencer_T111 16603-16636 Sentence denotes Butcher, personal communication).
TextSentencer_T112 16637-16863 Sentence denotes Whereas bacteria do not require access to the host cell cytoplasm for replication, many pathogens induce their own uptake to gain access to an immunologically protected environment that is optimal for survival and replication.
TextSentencer_T113 16864-17059 Sentence denotes Bacterial entry is a complex process that involves direct adherence to host cell receptors or indirect adherence through extracellular matrix ligands, followed by host-pathogen signalling events.
TextSentencer_T114 17060-17298 Sentence denotes Once internalized, some pathogens remain within vacuoles (Salmonella spp., Yersinia spp., Streptococcus spp., Neisseria spp.) [48] [49] [50] [51] , whereas others escape to infect neighbouring cells (Shigella spp., Listeria spp.) 52, 53 .
TextSentencer_T115 17299-17499 Sentence denotes Proteins that mediate the entry of bacteria into non-phagocytic host cells are known as invasins, the prototype of which is the Yersinia spp. invasin protein (InvA), which was discovered in 1987 (REF.
TextSentencer_T116 17500-17505 Sentence denotes 54 ).
TextSentencer_T117 17506-17561 Sentence denotes More recently, other invasins such as the Yersinia spp.
TextSentencer_T118 17562-17645 Sentence denotes YadA and Neisseria meningitidis NadA have been described [55] [56] [57] [58] [59] .
TextSentencer_T119 17646-17873 Sentence denotes YadA and NadA, together with the ubiquitous surface proteins UspA1 and UspA2 of Moraxella catarrhalis, represent the prototypes of the Oca (oligomeric coiled-coil adhesin) family of putative non-fimbrial adhesins 60 (TABLE 1) .
TextSentencer_T120 17874-18122 Sentence denotes Genome sequence analysis and structural prediction algorithms have identified more than 20 novel members of this family in Gram-negative bacteria, as well as in plant pathogens 60, 61 , all of which share several structural and functional features.
TextSentencer_T121 18123-18280 Sentence denotes Oca family proteins are grouped by homologies found in the C-terminal anchor domain, but how did diverse bacterial species acquire these cell entry machines?
TextSentencer_T122 18281-18476 Sentence denotes As suggested by the anomalous GC composition of the oca genes, and by the conserved nature of their C-terminal domains, we propose that these domains might have originated by horizontal transfer.
TextSentencer_T123 18477-18732 Sentence denotes A possible origin could be envisaged in the ubiquitous siphoviridae P-Eib prophages, which encode a family of four genes (eib-A, -C, -D and -E), the protein products of which confer immunoglobulin-binding activity to the ECOR group of E. coli strains 62 .
TextSentencer_T124 18733-18820 Sentence denotes The Eib (E. coli immunoglobulin binding) proteins form high-molecular-weight oligomers.
TextSentencer_T125 18821-18879 Sentence denotes They show the same YadA-like tripartite organization (FIG.
TextSentencer_T126 18880-19062 Sentence denotes 2e) centred on a core coiled-coil motif with a C-terminal membrane anchor that shares sequence identity with the corresponding domains of UspA2 (60.3%),YadA (56.7%) and NadA (58.6%).
TextSentencer_T127 19063-19152 Sentence denotes One hypothesis is that eib genes were transferred among E. coli strains by phage vectors.
TextSentencer_T128 19153-19342 Sentence denotes A similar mechanism of prophage-driven transfer might have been involved in the propagation of these surface molecules (or of their anchor domains) to different recipient bacterial species.
TextSentencer_T129 19343-19523 Sentence denotes Support for this idea comes from the fact that some of the genes that code for proteins of the Oca family, such as YadA and NadA, are carried on mobile genetic elements (TABLE 1) .
TextSentencer_T130 19524-19720 Sentence denotes In addition to theories of evolutionary origins, we provide further evidence that bacterial invasins have a role in cell entry that is similar to that mediated by viral fusion proteins and SNAREs.
TextSentencer_T131 19721-19745 Sentence denotes Structural similarities.
TextSentencer_T132 19746-20007 Sentence denotes Like most class I, class II and non-enveloped viral spike proteins, YadA and NadA are expressed as homotrimers on the surface of Yersinia spp. and N. meningitidis, respectively, and they participate in the binding to and uptake of the bacterium into host cells.
TextSentencer_T133 20008-20228 Sentence denotes Despite the lack of complete three-dimensional structures for proteins of the Oca family, much has been learned about the topology of these proteins through ultramicroscopy and primary and secondary structure prediction.
TextSentencer_T134 20229-20436 Sentence denotes Similar to viral spike proteins, both YadA and UspA appear as distinct 'lollipop'-shaped structures, forming a halo-like surface projection on the outer membrane of the bacteria in electron micrographs (FIG.
TextSentencer_T135 20437-20442 Sentence denotes 2e) .
TextSentencer_T136 20443-20637 Sentence denotes Whereas the shape of the projections seems similar, the rod-like segments are three times longer in UspA compared with YadA, which extends approximately 230Å from the bacterial cell surface 60 .
TextSentencer_T137 20638-20740 Sentence denotes This structure is reminiscent of the spike proteins that are expressed by many enveloped viruses (FIG.
TextSentencer_T138 20741-20748 Sentence denotes 2c,d) .
TextSentencer_T139 20749-20960 Sentence denotes Furthermore, sequence analysis of YadA, NadA and the UspA proteins has helped to define the molecular architecture of this class of molecules, which is remarkably similar to that of many viral envelope proteins.
TextSentencer_T140 20961-21297 Sentence denotes According to these predictions, three main domains can be envisaged for proteins of the Oca family: a C-terminal outer membrane anchor domain; a rod-like intermediate segment formed mainly by extended right-or change that is known to trigger the recruitment of effector molecules, such as focal adhesion kinase (FAK), to the entry site.
TextSentencer_T141 21298-21404 Sentence denotes Both bacterial and viral pathogens use the cell and its effector molecules to induce intracellular uptake.
TextSentencer_T142 21405-21605 Sentence denotes Pathogens not only depend on the host cell machinery for their internalization, but also for trafficking within the cytoplasm and for the ability to find sites that allow replication and transmission.
TextSentencer_T143 21606-21780 Sentence denotes Endosomal trafficking and exocytosis of secretory vesicles use molecular mechanisms and signalling pathways that are subverted by bacteria and viruses for their own purposes.
TextSentencer_T144 21781-21909 Sentence denotes Exocytosis and endocytic events involve docking factors such as the exocyst protein complex and Rab GTPases, such as Rab3A (FIG.
TextSentencer_T145 21910-21915 Sentence denotes 3a) .
TextSentencer_T146 21916-22097 Sentence denotes Vesicle trafficking also involves the activation of intracellular cytoskeleton effector molecules such as phosphatidylinositol 3-kinase (PI3K) and other small GTPases such as Cdc42.
TextSentencer_T147 22098-22206 Sentence denotes During the final stages of exocytosis, F-actin forms a cortical network under the plasma membrane of a cell.
TextSentencer_T148 22207-22400 Sentence denotes It has been shown that exocytotic vesicles are transported along microtubules to the plasma membrane, but are not secreted before the cortical actin network opens locally to form the exit pore.
TextSentencer_T149 22401-22564 Sentence denotes Also, PI3K activates phosphatidylinositol 4,5-bisphosphate (PIP 2 ), which has been implicated in the regulation of the actin cytoskeleton and vesicle trafficking.
TextSentencer_T150 22565-22748 Sentence denotes PIP 2 stimulates de novo actin polymerization All these proteins form high-molecularweight oligomers, have a role in cell attachment, mediate serum resistance and are good immunogens.
TextSentencer_T151 22749-22848 Sentence denotes Gram-positive organisms have also evolved strategies that facilitate host cell adherence and entry.
TextSentencer_T152 22849-23158 Sentence denotes Similar to SNAREs and viral membrane fusion proteins, a group of Gram-positive bacterial adhesins are known to undergo a conformational change on receptor binding, which brings the molecule from a disordered to an ordered state, therefore reinforcing binding and facilitating subsequent cell invasion 73, 74 .
TextSentencer_T153 23159-23278 Sentence denotes Proteins that mediate these functions also share a fibrillike elongated architecture, usually composed of coiled coils.
TextSentencer_T154 23279-23596 Sentence denotes Examples of such proteins include the well characterized dimeric M protein of Streptococcus pyogenes 75 , the fibronectin binding protein (FnbA) of Streptococcus dysgalactiae, the fibrinogen binding protein (FgbP) of Streptoccoccus equi 76, 77 , and the choline binding protein (CbpA) of Streptococcus pneumoniae 78 .
TextSentencer_T155 23597-23737 Sentence denotes The M protein of S. pyogenes is a fibrillar molecule that binds to fibrinogen and albumin and promotes bacterial adhesion to host cells 75 .
TextSentencer_T156 23738-23955 Sentence denotes Interestingly, FnbA and structurally similar proteins that are produced by Staphylococcus aureus and S. pyogenes mediate bacterial cell entry by binding to integrins through a fibronectin-based bridging mechanism 79 .
TextSentencer_T157 23956-24070 Sentence denotes This mechanism involves a conformation As with many virulence factors, YadA is located on the 70-kD plasmid (pYV).
TextSentencer_T158 24071-24117 Sentence denotes Unlike the β-immunoglobulin-like Yersinia spp.
TextSentencer_T159 24118-24217 Sentence denotes InvA, YadA is a homotrimer that is induced during exponential growth in minimal media at 37°C (REF.
TextSentencer_T160 24218-24223 Sentence denotes 72 ).
TextSentencer_T161 24224-24335 Sentence denotes In vitro,YadA binds collagen, laminin, cellular fibronectin, intestinal submucosa and hydrophobic surfaces 70 .
TextSentencer_T162 24336-24573 Sentence denotes Single amino-acid mutations in the N-terminal receptor-binding domain resulted in the abrogation of YadA binding to extracellular matrix proteins in vitro, which led to a marked reduction in virulence in an animal model of infection 63 .
TextSentencer_T163 24574-24731 Sentence denotes Eitel and Dersch argue that YadA belongs to a secondary uptake pathway that might complement InvAmediated cell entry when synthesis of InvA is repressed 72 .
TextSentencer_T164 24732-24912 Sentence denotes Earlier reports showed that yadA genes that were encoded on the pYV plasmid promoted internalization of Yersinia invA mutants, but with a lower frequency of occurrence 55, 57, 71 .
TextSentencer_T165 24913-25162 Sentence denotes More recent studies provide evidence that E. coli strains that express YadA under the pBAD-inducible arabinose promoter, in gentamicin protection assays, had the same ability to adhere to and enter cell monolayers as E. coli that expressed InvA 72 .
TextSentencer_T166 25163-25251 Sentence denotes Recombinant NadA mediates binding and uptake of E. coli into Chang epithelial cells 59 .
TextSentencer_T167 25252-25294 Sentence denotes It also has strong immunogenic properties.
TextSentencer_T168 25295-25375 Sentence denotes Little information is available on the biological function of the UspA proteins.
TextSentencer_T169 25376-25458 Sentence denotes Nevertheless, they seem to share central functional properties with YadA and NadA.
TextSentencer_T170 25460-25570 Sentence denotes Contain an N-terminal signal peptide Contain an N-terminal signal peptide Contain an N-terminal signal peptide
TextSentencer_T171 25571-25770 Sentence denotes The majority of the protein complex is exposed The majority of the fusion protein is exposed Surface exposed Unknown High density on the viral membrane Might have a high density on bacterial membrane
TextSentencer_T172 25771-25908 Sentence denotes The anchor domain is a predicted hydrophobic The anchor domain is a hydrophobic α-helix The anchor domain is typically a β-barrel α-helix
TextSentencer_T173 25909-26277 Sentence denotes Stalk comprised of heterotrimers that contain Stalk comprised of antiparallel α-coils Stalk comprised of α-coils and heptad repeats α-coils and heptad repeats and heptad repeats NA N-terminal domain confers receptor N-terminal domain confers binding, serum recognition and binding resistance, agglutination, complement inhibition, and activation of signal transduction
TextSentencer_T174 26278-26590 Sentence denotes Complex forms a rod-like structure comprised Form higher-order oligomers (homotrimers) Form higher-order oligomers (mainly homotrimers) of a parallel four-helix bundle of α-coils by activating a pathway that comprises the Wiskott-Aldrich syndrome protein (WASP) and the actin-related protein complex ARP2/3 (FIG.
TextSentencer_T175 26591-26595 Sentence denotes 3) .
TextSentencer_T176 26596-26763 Sentence denotes Other studies show that actin polymerizes from cholesterol-sphingolipid-rich membrane microdomains called 'rafts' , in a tyrosine phosphorylation-dependent manner 80 .
TextSentencer_T177 26764-26884 Sentence denotes Productive viral and bacterial infections are also frequently associated with profound changes of the host cytoskeleton.
TextSentencer_T178 26885-26971 Sentence denotes Such changes are often mediated through phosphorylation-regulated signalling cascades.
TextSentencer_T179 26972-27239 Sentence denotes Similar to SNARE-mediated intracellular trafficking, some viral uptake mechanisms involve a tightly controlled interplay of intracellular molecules such as clathrinan effector protein that interacts with intracellular transport effector molecules, such as Esp15 (REF.
TextSentencer_T180 27240-27291 Sentence denotes 81 ), amphiphysin and the AP2 adaptor proteins 82 .
TextSentencer_T181 27292-27522 Sentence denotes For example, during cell entry, the influenza virus might be taken up by a clathrin-dependent or clathrin-independent endocytic route, following the initial interaction of viral haemagglutinin with its sialicacid receptor 17, 83 .
TextSentencer_T182 27523-27750 Sentence denotes Also, in vitro data indicate that the GTPase dynamin, which is known to be involved in the release of endosomes from the plasma membrane, is also essential in the early events of influenza virus endocytosis [84] [85] [86] (FIG.
TextSentencer_T183 27751-27756 Sentence denotes 3b) .
TextSentencer_T184 27757-27904 Sentence denotes The role of actin in the endocytosis of viruses is not clear, although a role for actin in viral exocytosis and budding has been described 28, 87 .
TextSentencer_T185 27905-28012 Sentence denotes Microtubules might also be involved in these processes, as seen in the trancytosis of HIV in vitro 22, 88 .
TextSentencer_T186 28013-28222 Sentence denotes Furthermore, HIV is known to activate a FAK pYK2 kinase and to signal to the mitogen-activated protein kinase (MAPK) pathway 88 , which is important in the uptake and intracellular transport of the virus (FIG.
TextSentencer_T187 28223-28228 Sentence denotes 3b) .
TextSentencer_T188 28229-28554 Sentence denotes Signalling is a common theme in cell entry, as internalization of the adenovirus through ligand binding to its co-receptor integrin activates both protein kinase C and PI3K 89 , as well as subsequent effector molecules that are involved in vesicular trafficking (Rab5) and cytoskeletal organization (Rac1, Cdc42 and dynamin).
TextSentencer_T189 28555-28732 Sentence denotes Interestingly, pre-treatment of epithelial cells with cytochalasin D, a product that disrupts actin fibres, causes a dose-dependent inhibition of adenovirus internalization 89 .
TextSentencer_T190 28733-28934 Sentence denotes These results indicate that assembly of the actin cytoskeleton plays a key part in viral endocytosis, and therefore resembles the general mechanism of invasion that is used by many bacterial pathogens.
TextSentencer_T191 28935-29235 Sentence denotes Bacterial internalization is accompanied by changes in the phosphorylation status of cytoskeleton effector molecules and scaffolding proteins 6 As bacterial entry does not involve fusion between bacterial and host plasma membranes, we do not yet have an explanation for all the similarities observed.
TextSentencer_T192 29236-29537 Sentence denotes However, recent data indicates that, even in viruses, these molecular machines are used for common cell entry mechanisms and not solely for membrane fusion events -non-enveloped rotaviruses do not fuse but instead disrupt the host cell membrane, thereby allowing the virion access to the cytoplasm 5 .
TextSentencer_T193 29538-29804 Sentence denotes The mechanism of cell entry that is exploited by this class of viruses might represent the missing link between viral and bacterial cell-entry mechanisms and might help to explain the possible mechanism of invasion that is promoted by coiled-coil bacterial invasins.
TextSentencer_T194 29805-30011 Sentence denotes The most probable and supported hypothesis is that, after mediating adhesion, NadA and YadA undergo a conformational change and bring the bacterial and host membranes into tight contact (intimate adhesion).
TextSentencer_T195 30012-30223 Sentence denotes This process would initiate the bacterial-host signalling events that induce actin polymerization, formation of membrane protrusions around the bacteria, and ultimately result in bacterial uptake by endocytosis.
TextSentencer_T196 30224-30461 Sentence denotes A less likely possibility is that these bacterial invasins function as real fusion proteins by binding the membrane protrusions that surround the bacteria, bringing them together until they fuse and engulf the bacteria into the endosome.
TextSentencer_T197 30462-30665 Sentence denotes The discovery of a large family of bacterial proteins with structural and potentially functional similarities to viral spikes and SNAREs indicates that pathogens use a recurrent theme to cross membranes.
TextSentencer_T198 30666-30801 Sentence denotes These common machineries might confer a selective advantage to the pathogen and provide a significant contribution to pathogen fitness.
TextSentencer_T199 30802-30899 Sentence denotes Other examples of similar viral and bacterial cell-entry structures have recently been described.
TextSentencer_T200 30900-31130 Sentence denotes The first is IncA of Chlamydia trachomatis, a coiled-coil protein that has been shown to assemble into tetramers and to interact homotypically to promote a vesicle fusion mechanism that is similar to that of eukaryotic SNAREs 95 .
TextSentencer_T201 31131-31268 Sentence denotes The second example is the structural resemblance between the major coat protein of the bacteriophage PRD1 and the human adenovirus Hexon.
TextSentencer_T202 31269-31461 Sentence denotes Although the two proteins have different amino-acid sequences, they show an identical topology and are organized in a doublebarrel trimer that contains two eightstranded JELLY-ROLL MOTIFS 96 .
TextSentencer_T203 31462-31688 Sentence denotes We have no doubt that evolutionary pressure has selected machineries with similar architectural domains to perform similar functions in bacteria, viruses and eukaryotic cells, but the absence of any primary sequence similarity
TextSentencer_T204 31689-31974 Sentence denotes In conclusion, both InvA-promoted and YadA-promoted cell entry occur through a 'zipper-like' mechanism; that is, a high affinity-binding event that takes advantage of phosphorylation-regulated signalling pathways and that requires the action of phosphokinases and actin polymerization.
TextSentencer_T205 31975-32101 Sentence denotes Recent experimental data from the NadA protein indicates that, similar to YadA, NadA-mediated invasion is actin-dependent 59 .
TextSentencer_T206 32102-32362 Sentence denotes These results indicate that many of the signalling cascades described in pathogen uptake and eukaryotic vesicle trafficking converge on the machinery involved in host cell reorganization, providing new theories on the evolution of pathogen survival strategies.
TextSentencer_T207 32363-32557 Sentence denotes In this report, we provide evidence that a large family of bacterial surface proteins has an overall modular organization that resembles membrane fusion proteins such as viral spikes and SNAREs.
TextSentencer_T208 32558-32740 Sentence denotes Two bacterial membrane proteins, YadA and NadA, have specifically been shown to mediate bacterial entry into host cells, a function that is analogous to that of viral spike proteins.
TextSentencer_T209 32741-33057 Sentence denotes The data available on the mechanism of invasion promoted by YadA and NadA, compared with what is known about viral uptake, allow some speculation on a possible common route of cell entry that is shared by viruses and bacteria. so far, there is no data on the signalling events that occur in YadA-mediated cell entry.
TextSentencer_T210 33058-33273 Sentence denotes It is known that, following tight adhesion of Yersinia spp. to the host cellular surface, InvA-mediated bacterial uptake seems to involve FAK 125 , Src, PI3K, the small GTPase Rac1 and the ARP2/3 complex 90,91 (FIG.
TextSentencer_T211 33274-33279 Sentence denotes 3c) .
TextSentencer_T212 33280-33521 Sentence denotes Similarly, recent data support the hypothesis that YadA-mediated bacterial invasion is dependent on protein phosphorylation events, as the addition of tyrosine kinase inhibitors strongly impairs Yersinia spp. cell entry through YadA 72, 92 .
TextSentencer_T213 33522-33723 Sentence denotes InvA-and YadA-promoted cell entry occurs through the interaction with the β1-integrins 66 and the interaction of YadA with the β1-integrins is mediated through collagen and fibronectin [68] [69] [70] .
TextSentencer_T214 33724-34029 Sentence denotes On the basis of in vitro experiments that describe collagen signal transduction, one might infer that YadAmediated cell entry is dependent on cell signalling -collagen IV and laminin, but not fibronectin, are known to stimulate tyrosine phosphorylation of intracellular FAK and other signalling molecules.
TextSentencer_T215 34030-34234 Sentence denotes Notably, one of the molecules involved in the InvA signalling pathway, PI3K, is implicated in actin polymerization and can also interact with FAK 125 , which itself associates with β 1 -integrins 93, 94 .
TextSentencer_T216 34235-34316 Sentence denotes This implicates modulation of the actin cytoskeleton in YadA-mediated cell entry.
TextSentencer_T217 34317-34408 Sentence denotes A widely used technique for obtaining information about protein structure and conformation.
TextSentencer_T218 34409-34494 Sentence denotes It is a sensitive and reliable tool to study the structure and stability of proteins.
TextSentencer_T219 34495-34624 Sentence denotes An important protein-protein interaction motif often used to control oligomerization, characterized by a conserved heptad repeat.
TextSentencer_T220 34625-34712 Sentence denotes Coiled coils consist of helices that wrap around one another with a superhelical twist.
TextSentencer_T221 34713-34878 Sentence denotes A sequence of 20-30 mainly hydrophobic residues (Ala and Gly) found at the N-terminus of the stalk exposed after a conformational change of the viral fusion protein.
TextSentencer_T222 34879-34960 Sentence denotes Insertion of the peptide into the host cell membrane leads to cell fusion events.
TextSentencer_T223 34961-35091 Sentence denotes HEPTAD REPEAT Seven residue patterns denoted (abcdefg) n in which the a and d residues (core positions) are generally hydrophobic.
TextSentencer_T224 35092-35275 Sentence denotes As there are 3.6 residues to each turn of the α-helix, these a and d residues form a hydrophobic seam, which, as each heptad is slightly under two turns, slowly twists around a helix.
TextSentencer_T225 35276-35373 Sentence denotes Heptad repeats are characteristic of certain proteins such as the intermediate filament proteins.
TextSentencer_T226 35374-35457 Sentence denotes INVASIN Any bacterial surface protein that provokes endocytic uptake by host cells.
TextSentencer_T227 35458-35572 Sentence denotes Adhesins, on the other hand, promote binding to cell surface receptors, but do not elicit uptake by the host cell.
TextSentencer_T228 35573-35671 Sentence denotes These motifs are found in proteins in which the primary fold contains only β-antiparallel strands.
TextSentencer_T229 35672-35828 Sentence denotes Like other elements of super-secondary structure involving the β-strand (for example, the β-α-α-β unit) the known structure forms a right-handed superhelix.
TextSentencer_T230 35829-36011 Sentence denotes The first formal classification scheme was created by Carolus Linnaeus and relied on classification of species according to hierarchical structure, from most general to most similar.
TextSentencer_T231 36012-36158 Sentence denotes However, this scheme ignores their evolutionary history, and important aspects of the origin of those similarities and differences are overlooked.
TextSentencer_T232 36159-36250 Sentence denotes Soluble NSF (N-ethylmaleimide-sensitive fusion protein) accessory protein (SNAP) receptor).
TextSentencer_T233 36251-36350 Sentence denotes These proteins contain a heptad repeat of 60-90 residues that participate in coiled-coil formation.
TextSentencer_T234 36351-36424 Sentence denotes The family of SNARE proteins are involved in intracellular fusion events.
TextSentencer_T235 36425-36567 Sentence denotes This method uses computer modelling to obtain structural information based on the amino-acid sequence of an uncharacterized protein structure.
TextSentencer_T236 36568-36779 Sentence denotes Threading analysis is mostly used to detect remote homologues that can not be detected by standard sequence alignment. leaves open the question of whether this is the result of convergent or divergent evolution.
TextSentencer_T237 36780-36886 Sentence denotes In the first case, a similar architecture would be a common solution for molecules with different origins.
TextSentencer_T238 36887-37113 Sentence denotes In the second case, the morphology that is necessary for function would be the only remaining feature from an ancestral molecule and, as suggested by the LINNAEAN APPROACH, "morphology might be the real link to phylogeny" 97 .
TextSentencer_T239 37114-37319 Sentence denotes The main limits to our hypothesis relate to the lack of structural information on Oca bacterial invasins, and the dearth of experimental data on the mechanistic processes that lead to bacterial cell entry.
TextSentencer_T240 37320-37509 Sentence denotes However, structural prediction on YadA and NadA and recent experimental results on NadA support a close resemblance between class I and non-enveloped viral spike proteins and Oca molecules.
TextSentencer_T241 37510-37764 Sentence denotes The fact that class II viral fusion proteins are functionally related to class I viral fusion proteins, despite the lack of structural similarities, leads us to speculate that microorganisms have found various solutions to the problem of host cell entry.
TextSentencer_T242 37765-37910 Sentence denotes Hopefully, this Opinion article will stimulate further experimentation and will help to unveil more bacterial examples of cell entry machineries.
TextSentencer_T243 37911-38248 Sentence denotes It is fascinating to think that we might be able to exploit these perfect molecular machineries to develop novel antimicrobial drugs such as the HIV fusion inhibitor, or for the development of novel nanomachines that would use programmed fusion between membrane-bound vesicles for drug delivery and for in vivo targeting of cancer cells.
TextSentencer_T244 38249-38410 Sentence denotes Preliminary data also indicates that functional domains of bacterial and viral entry proteins can be exchanged to obtain chimeric proteins with novel properties.
TextSentencer_T245 38411-38711 Sentence denotes Future studies to resolve the crystal structure, identify structural rearrangements involved in conformational changes, as well as to understand the intracellular signalling events mediated by the Oca family of proteins will be crucial in elucidating the speculative function of this set of proteins.