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PubMed2004

Crystal structure of the flagellar sigma/anti-sigma complex sigma(28)/FlgM reveals an intact sigma factor in an inactive conformation.

The key regulators of bacterial transcription initiation are the sigma factors, which direct promoter recognition and melting but only after binding to the core RNA polymerase to form the holoenzyme. X-ray crystal structures of the flagellar sigma, sigma(28), in complex with its anti-sigma, FlgM, explain the inhibition mechanism of FlgM, including its ability to attack and destabilize the sigma(28)-holoenzyme. The sigma domains (sigma(2), sigma(3), and sigma(4)) pack together in a compact unit with extensive interdomain interfaces that bury the promoter binding determinants, including the -35 element recognition helix of sigma(4), which fits in an acidic groove on the surface of sigma(3). The structure illustrates the large rearrangements that sigma(28) must undergo to form the holoenzyme and provides insights into the regulation of sigma(28) promoter binding activity that may extend, at least in principle, to other sigmas.

Amino Acid Sequence↗
PubMed1980

Flagellar roots, mating structure and gametic fusion in the green alga Ulva lactuca (Ulvales).

The slightly anisogamous gametes of Ulva lactuca exhibit a cruciate flagellar root system consisting of 4 microtubular roots (4-2-4-2 system) and an elaborate system of fibrous roots associated with the 2-stranded microtubular roots. Two fibres (32-nm striation periodicity; system I fibres) closely underlie each of the 2-stranded roots, while different fibres (150-nm striation periodicity; system II fibres) run parallel to the root microtubules, and are 150-200 nm more internally located. Female gametes have 4 system II fibres, 3 of which are combined into a compound fibre associated with one microtubular root, while the fourth fibre is associated with the opposite root. In male gametes only 2 system II fibres are present, each underlying one of the two 2-stranded roots. A special region of the plasmalemma of both gamete types about 0.5 mum away from the basal bodies and located between 2 adjacent microtubular roots is structurally specialized and acts as a mating structure in gametic fusion. The region is oval-shaped and up to I.I mum long with a maximum diameter of 0.7 mum. A continuous electron-dense boundary layer underlies the plasmalemma at the edges of the mating structure. In both gamete types the mating structure consists of a fuzzy layer of material underlying the plasmalemma and special granules (60 nm diameter) are associated with this layer on its cytoplasmic side. In addition diffuse material overlies the mating structure, especially in male gametes. The mating structure is connected to 3 different kinds of flagellar roots: the boundary layer is linked to a 2-stranded microtubular root and its associated system I fibre; the fuzzy layer of the mating structure is connected with a system II fibre; and in female gametes this is the compound system II fibre. The ultrastructural changes which occur after mixing the 2 gamete types have been followed. Mating structure activation involves contraction of system II fibres (change of striation periodicity to 100 nm), detachment of special granules from the fuzzy layer of the mating structure and their replacement by electron-transparent vesicles at the prospective cell fusion site. Furthermore, release of electron-dense contents from Golgi-derived vesicles in the anterior part of both gamete types precedes cell fusion. Cell fusion is exclusively initiated in a region delimited by the 2 mating structures. After partial dissolution the 2 plasma membranes unite within the mating structure regions. The ultrastructure of gametic fusion in Ulva lactuca is compared to that of other green algae and the significance of flagellar roots in the mating process of green algae is discussed.

Chlorophyta↗
PubMed1985

Structure of complex flagellar filaments in Rhizobium meliloti.

The complex flagella of Rhizobium meliloti 2011 and MVII-1 were analyzed with regard to serology, fine structure, subunits, and amino acid composition. The serological identities of flagellar filaments of the two strains were demonstrated by double immunodiffusion with antiflagellin antiserum. The filaments had a diameter of 16 nm. Their morphology was dominated by the prominent undulations of an external three-start helix running at a 10-nm axial distance and at an angle of 32 degrees. Faint nearly axial striations indicated the presence of a tubular core of a different helical order. The complex filaments consisted of 40,000-dalton flagellin monomers. Typically, the amino acid composition was 3 to 4% higher in nonpolar residues and 5 to 7% lower in aspartic and glutamic acids (and their amides) than that of plain flagellar proteins. There were no immunochemical relationships among Pseudomonas rhodos, Rhizobium lupini, and R. meliloti complex flagella, suggesting that the latter represent a new class.

Amino Acids↗
PubMed1987

[Similarity of Vibrio alginolyticus, V. cholerae and other Vibrio species with respect to the structure of their flagellar apparatus and ribosomal 5S-RNA].

Electron microscopic analysis of basal bodies of the flagella Vibrio alginolyticus revealed a structure composed of four discs. The diameters of two discs localized in the cytoplasmic membrane appeared to be twice as little as those of the other two discs. In this respect the basal body of V. alginolyticus resembles that of V. cholerae. The 5S sequence of ribosomal RNA from V. alginolyticus appeared to be similar to those of V. cholerae, V. harveyi and some other vibrios. Comparison of 5S-RNA sequence culminated in a dendrogram of evolutionary relationships of various bacterial species, suggesting that V. alginolyticus is a typical representative of the Vibrionacea family. The data obtained are discussed in terms of the role of Na+ energy metabolism in living cells.

Flagella↗
PubMed1977

Flagellar elongation and shortening in Chlamydomonas. III. structures attached to the tips of flagellar microtubules and their relationship to the directionality of flagellar microtubule assembly.

Two structures on the distal ends of Chlamydomonas flagellar microtubules are described. One of these, the central microbutule cap, attaches the distal ends of the central pair microtubules to the tip of the flagellar membrane. In addition, filaments, called distal filaments, are observed attached to the ends of the A-tubules of the outer doublet microtubules. Inasmuch as earlier studies suggested that flagellar elongation in vivo occurs principally by the distal addition of sublnits and because it has been shown that brain tubulin assembles in vitro primarily onto the distal ends of both central and outer doublet microtubules, the presence of the cap and distal filaments was quantitated during flagellar resorption and elongation. The results showed that the cap remains attached to the central microtubules throughout flagellar resorption and elongation. The cap was also found to block the in vitro assembly of neurotubules onto the distal ends of the central microtubules. Conversely, the distal filaments apparently do not block the assembly of neurotubules onto the ends of the outer doublets. During flagellar elongation, the distal ends of the outer doublets are often found to form sheets of protofilaments similar to those observed on the elongating ends of neurotubules being assembled in vitro. These results suggest that the outer doublet microtubules elongate by the distal addition of subunits, whereas the two central microtubules assemble by the addition of subunits to the proximal ends.

Chlamydomonas↗
PubMed1987

Three-dimensional structure of the complex flagellar filament of Rhizobium lupini and its relation to the structure of the plain filament.

Electron micrographs of negatively stained preparations were used to obtain a three-dimensional reconstruction of the complex flagellar filament of Rhizobium lupini H13-3. The complex filament has an organization similar to that of the more common plain filament, but the subunits are perturbed in a pairwise fashion to generate a very distinctive set of three continuous ridges of density along the outer surface of the filament. In the three-dimensional map, the design of the complex filament is similar to that of the plain filament described in the accompanying paper. The structures consist of 11 segmented rods of density lying at a radius of 65 to 70 A. The exterior surfaces of both kinds of filaments consist of features that protrude from the segmented rods. The interiors of both consist of arms that extend inwards from the rods. In the case of the complex filament, but not of the plain filament, the inner arms interact to generate three tubular features, which, together with the three outer ridges, may account for the more brittle and, by implication, stiffer nature of the complex filament.

Computer Simulation↗
PubMed2005

Crystal structure of the flagellar rotor protein FliN from Thermotoga maritima.

FliN is a component of the bacterial flagellum that is present at levels of more than 100 copies and forms the bulk of the C ring, a drum-shaped structure at the inner end of the basal body. FliN interacts with FliG and FliM to form the rotor-mounted switch complex that controls clockwise-counterclockwise switching of the motor. In addition to its functions in motor rotation and switching, FliN is thought to have a role in the export of proteins that form the exterior structures of the flagellum (the rod, hook, and filament). Here, we describe the crystal structure of most of the FliN protein of Thermotoga maritima. FliN is a tightly intertwined dimer composed mostly of beta sheet. Several well-conserved hydrophobic residues form a nonpolar patch on the surface of the molecule. A mutation in the hydrophobic patch affected both flagellar assembly and switching, showing that this surface feature is important for FliN function. The association state of FliN in solution was studied by analytical ultracentrifugation, which provided clues to the higher-level organization of the protein. T. maritima FliN is primarily a dimer in solution, and T. maritima FliN and FliM together form a stable FliM(1)-FliN(4) complex. Escherichia coli FliN forms a stable tetramer in solution. The arrangement of FliN subunits in the tetramer was modeled by reference to the crystal structure of tetrameric HrcQB(C), a related protein that functions in virulence factor secretion in Pseudomonas syringae. The modeled tetramer is elongated, with approximate dimensions of 110 by 40 by 35 Angstroms, and it has a large hydrophobic cleft formed from the hydrophobic patches on the dimers. On the basis of the present data and available electron microscopic images, we propose a model for the organization of FliN subunits in the C ring.

Amino Acid Motifs↗
PubMed2005

Refining the structure of the Halobacterium salinarum flagellar filament using the iterative helical real space reconstruction method: insights into polymorphism.

The eubacterial flagellar filament is an external, self-assembling, helical polymer approximately 220 A in diameter constructed from a highly conserved monomer, flagellin, which polymerizes externally at the distal end. The archaeal filament is only approximately 100 A in diameter, assembles at the proximal end and is constructed from different, glycosylated flagellins. Although the phenomenology of swimming is similar to that of eubacteria, the symmetry of the archebacterial filament is entirely different. Here, we extend our previous study on the flagellar coiled filament structure of strain R1M1 of Halobacterium salinarum. We use strain M175 of H.salinarum, which forms poly-flagellar bundles at high yield which, under conditions of relatively low ionic-strength (0.8 M versus 5 M) and low pH ( approximately 2.5 versus approximately 6.8), form straight filaments. We demonstrated previously that a single-particle approach to helical reconstruction has many advantages over conventional Fourier-Bessel methods when dealing with variable helical symmetry and heterogeneity. We show here that when this method is applied to the ordered helical structure of the archebacterial uncoiled flagellar filament, significant extensions in resolution can be obtained readily when compared to applying traditional helical techniques. The filament population can be separated into classes of different morphologies, which may represent polymorphic states. Using cryo-negatively stained images, a resolution of approximately 10-15 A has been achieved. Single alpha-helices can be fit into the reconstruction, supporting the proposed similarity of the structure to that of type IV bacterial pili.

Biopolymers↗
PubMed1992

Location of the basal disk and a ringlike cytoplasmic structure, two additional structures of the flagellar apparatus of Wolinella succinogenes.

The basal body of Wolinella succinogenes consists of a central rod, a set of two rings (L and P rings), a basal disk from 70 to 200 nm in diameter, and a terminal knob. In negatively stained preparations of flagellar hook-basal body complexes, some disks remain fixed perpendicularly to the grid and show that such a disk is located on the distal side of the P ring. The basal disks have been isolated with and without the P ring; in both cases there is a hole in the center of the disk. The diameter of the disk is smaller in the presence of the P ring. The L-P ring complex is therefore assumed to be a bushing for the rod. Thin sections of whole bacteria and spheroplasts reveal that the disk is attached to the inner surface of the outer membrane. At the insertions of the flagellar hook-basal body-basal disk complexes, depressions are visible in negatively stained preparations of whole bacteria and spheroplasts. A new ringlike structure is connected to an elongation of the basal body into the cytoplasm in both preparations. Its diameter (60 nm) is larger than that of the M ring. A heavily stained compartment can be seen in between the new ringlike structure and the basal disk, which may be formed by the energy transducing units.

Cytoplasm↗
PubMed2001

Structures of bacterial flagellar motors from two FliF-FliG gene fusion mutants.

Flagella purified from Salmonella enterica serovar Typhimurium contain FliG, FliM, and FliN, cytoplasmic proteins that are important in torque generation and switching, and FliF, a transmembrane structural protein. The motor portion of the flagellum (the basal body complex) has a cytoplasmic C ring and a transmembrane M ring. Incubation of purified basal bodies at pH 4.5 removed FliM and FliN but not FliG or FliF. These basal bodies lacked C rings but had intact M rings, suggesting that FliM and FliN are part of the C ring but not a detectable part of the M ring. Incubation of basal bodies at pH 2.5 removed FliG, FliM, and FliN but not FliF. These basal bodies lacked the C ring, and the cytoplasmic face of the M ring was altered, suggesting that FliG makes up at least part of the cytoplasmic face of the M ring. Further insights into FliG were obtained from cells expressing a fusion protein of FliF and FliG. Flagella from these mutants still rotated but cells were not chemotactic. One mutant is a full-length fusion of FliF and FliG; the second mutant has a deletion lacking the last 56 residues of FliF and the first 94 residues of FliG. In the former, C rings appeared complete, but a portion of the M ring was shifted to higher radius. The C-ring-M-ring interaction appeared to be altered. In basal bodies with the fusion-deletion protein, the C ring was smaller in diameter, and one of its domains occupied space vacated by missing portions of FliF and FliG.

Artificial Gene Fusion↗
PubMed1998

Quasi- and nonequivalence in the structure of bacterial flagellar filament.

In supercoiled forms of flagellar filaments, which are thought to be produced by combinations of two distinct subunit lattices, the lattices are elastically deformed in 11 different ways, depending on their azimuthal positions on the circumference of a tube with 11 protofilaments. Those two interactions are nonequivalent as opposed to quasiequivalent ones in elastically deformed lattices of otherwise identical interactions. The term nonequivalence is defined to represent different bonding interactions, and quasiequivalent is used to describe deformed but conserved bonding interactions. By using two distinct lattices that were accurately determined by x-ray fiber diffraction, 10 possible supercoiled forms of flagellar filaments were simulated, based on a bistable-subunit packing model. Comparison to the observed forms showed good agreement, indicating that the model and determined lattice parameters effectively represent realistic features of the structure. The simulated quasiequivalent lattices have been compared to the two nonequivalent lattices, revealing an interesting feature: the maximum deviation in the intersubunit distance by elastic deformation is almost three-quarters of the difference between the two distinct lattices, demonstrating a balanced coexistence of a well-defined conformational distinction and extensive adaptability in the molecular structure of flagellin and its packing interactions.

Bacteria↗
PubMed1995

Structure of bacterial flagellar filaments at 11 A resolution: packing of the alpha-helices.

Recent advances in the analysis of electron micrographs of frozen, hydrated bacterial filaments have allowed us to average data from more than 150 images and to reconstruct the bacterial flagellar filament of Salmonella typhimurium at a resolution of approximately 11 A. In addition to the outermost features seen in earlier lower resolution maps of the filament, we find a pair of concentric tubes which surround a approximately A diameter channel at the center of the structure. The walls of these tubes are composed of rod-like features which we have interpreted as columns of individual alpha-helices stacked end-to-end. Each column runs approximately parallel to the helix axis. The wall of the innermost tube, at a radius of approximately 20 A, is formed from 11 such columns. The wall of the second tube is formed from 22 columns which occur alternately at radii of approximately 43 and approximately 47 A. The two concentric tubes are held apart by spacers. These are short, rod-like features, which run approximately parallel to the helix axis. We have interpreted these as additional alpha-helices. By symmetry, each flagellin monomer contributes an alpha-helix to the inner tube, two alpha-helices to the outer tube and a fourth alpha-helix to the spacer. We have tentatively assigned one type of alpha-helix in the outer tube to the approximately 30 C-terminal residues of flagellin while the remaining three alpha-helices are assigned to the approximately 70 N-terminal residues. This interpretation of the reconstruction is consistent with available biochemical, biophysical and amino acid sequence information. We also present details of improved methodology to extract and evaluate the original data and also to assess the statistical significance of features in the three-dimensional map.

Bacterial Proteins↗
PubMed1991

New structural features of the flagellar base in Salmonella typhimurium revealed by rapid-freeze electron microscopy.

The structure of the flagellar base in Salmonella typhimurium has been studied by rapid-freeze techniques. Freeze-substituted thin sections and freeze-etched replicas of cell envelope preparations have provided complementary information about the flagellar base. The flagellar base has a bell-shaped extension reaching as far as 50 nm into the bacterial cytoplasm. This structure can be recognized in intact bacteria but was studied in detail in cell envelopes, where some flagella lacking parts of the bell were helpful in understanding its substructure. Structural relationships may be inferred between this cytoplasmic component of the flagellum and the recently described flagellar intramembrane particle rings as well as the structures associated with the basal body in isolated, chemically fixed flagella.

Flagella↗
PubMed1994

Isolation, characterization and structure of bacterial flagellar motors containing the switch complex.

A putative complex of the three switch proteins, FliG, FliM and FliN appears to be directly involved in torque generation and control of direction of rotation. We have developed a preparative procedure for flagellar motors that retains these proteins as evidenced by Western blots using anti-FliG, anti-FliM and anti-FliN antibodies. Immunogold labeling with these three antibodies shows that the three switch proteins are localized to the motor. Electron micrographs of frozen-hydrated preparations reveal a large, new component we have termed the "C ring complex" attached to the cytoplasmic face of the M ring. In a three-dimensional reconstruction of the cylindrically averaged structure, the M-S ring complex appears thicker and wider by the addition of extra material to the cytoplasmic surface of the M ring. In addition, extending into the cytoplasm from the thickened M ring is the C ring complex, a thin-walled cylinder having a length of 170 A and an outer diameter of 450 A compared to the 290 A diameter of the M ring. We provide evidence that the thickened M ring contains FliG and that the C ring complex may contain FliM and FliN. The large diameter of the C ring complex may permit interaction with the M ring and with the circlet of studs thought to be the MotA/MotB complex.

Bacterial Proteins↗
PubMed1985

Structural genes for flagellar hook-associated proteins in Salmonella typhimurium.

The flaW, flaU, and flaV genes of Salmonella typhimurium LT2 were cloned into pBR322. These genes were mapped on the cloned DNA fragments by restriction endonuclease analysis and construction of the deletion derivatives. Their gene products were identified, by the minicell method, as proteins whose molecular weights were estimated to be 59,000 for the flaW product, 31,000 for the flaU product, and 48,000 for the flaV product. These values are identical to those of three species of hook-associated proteins (HAPs), namely, HAP1, HAP3, and HAP2. Furthermore, antibodies against HAP1, HAP3, and HAP2 specifically reacted with the gene products of flaW, flaU, and flaV, respectively. Therefore, we concluded that they are structural genes for HAPs. The antibodies against HAP1 and HAP3 also specifically reacted with the gene products of flaS and flaT of Escherichia coli, respectively. This indicates that these gene products are HAPs in E. coli. This result is consistent with the demonstration that flaS and flaT of E. coli are functionally homologous with flaW and flaU of S. typhimurium.

Bacterial Proteins↗
PubMed1980

Building bacterial flagella.

Most bacterial movement is the result of the action of a subcellular structure, the flagellar organelle. Bacterial flagella propel the cell by rotating, and this rotation is regulated in response to information transmitted by chemoreceptors on the surface of the cell. Rotation is driven by a motor anchored in the cell membrane. To understand such processes as the assembling of flagellar organelles, energy transduction to produce flagellar rotation, and the integration of sensory information necessary for chemotaxis, one prerequisite is the determination of the architecture of flagella. Emphasis is given here to experimental approaches using Escherichia coli and Salmonella in order to identify the flagellar components and to determine how these components are used to construct the functional organelle. The purification of apparently intact organelles has revealed an intricate structure composed to at least 11 polypeptide components. Genetic techniques have been developed which enable the identification of the components of the flagellar system. More than 35 genes which are necessary for flagellar function have been defined in E. coli, and the gene products of 17 of the genes have been identified. From such genetic studies, it is apparent that the flagellar system is complex and includes many elements in addition to those found in the intact flagellar structures purified from the cell membrane. Proteins required for energy and sensory transduction have been identified and located in the cytoplasm and cell membrane. Since these components are not integral parts of the isolated organelle, it is clear that flagellar movement requires the interaction of several functionally distinct and spatially separate systems. The organelle appears to be constructed in discrete stages consisting of the sequential association of individual components. As with bacteriophage assembly, some flagellar proteins function not as structural components, but to regulate the assembly of the organelle. A structural variation is found in Salmonella, which have the ability to alternately express one of two components of the flagellar filament. The unique genetic control mechanism regulating this structural variation is discussed.

Bacterial Physiological Phenomena↗
PubMed2005

A partial atomic structure for the flagellar hook of Salmonella typhimurium.

The axial proteins of the bacterial flagellum function as a drive shaft, universal joint, and propeller driven by the flagellar rotary motor; they also form the putative protein export channel. The N- and C-terminal sequences of the eight axial proteins were predicted to form interlocking alpha-domains generating an axial tube. We report on an approximately 1-nm resolution map of the hook from Salmonella typhimurium, which reveals such a tube made from interdigitated, 1-nm rod-like densities similar to those seen in maps of the filament. Atomic models for the two outer domains of the hook subunit were docked into the corresponding outermost features of the map. The N and C termini of the hook subunit fragment are positioned next to each other and face toward the axis of the hook. The placement of these termini would permit the residues missing in the fragment to form the rod-like features that form the core domain of the hook. We also fit the hook atomic model to an approximately 2-nm resolution map of the hook from Caulobacter crescentus. The hook protein sequence from C. crescentus is largely homologous to that of S. typhimurium except for a large insertion (20 kDa). According to difference maps and our fitting, this insertion is found on the outer surface of the hook, consistent with our modeling of the hook.

Amino Acid Sequence↗