Regulation of Bacillus subtilis macrofiber twist development by D-cycloserine.

The effect of D-cycloserine on the establishment of twist states in Bacillus subtilis macrofibers was examined. Macrofibers produced in the presence of the drug differed in twist compared with those produced in its absence. The degree of twist alteration was dependent on the concentration of D-cycloserine in the growth medium. Macrofibers of different twist states representative of the entire twist spectrum from tight left-handedness to tight right-handedness were produced in strains FJ7 and C6D in four different ways: by control of the concentration of D-alanine, magnesium sulfate, or ammonium sulfate in the growth medium or by control of the growth temperature. The structures so produced were used to determine the effect of D-cycloserine on twist establishment starting from different twist states throughout the twist spectrum. In all but one case, twist resulting from growth in the presence of D-cycloserine was further towards the left-hand end of the twist spectrum than that produced in its absence, the exception being the unusual left-handed twist states produced in strains C6D and the closely related RHX 11S at high D-alanine concentrations described here. Studies of the interaction between D-cycloserine and D-alanine both used alone and used independently with the other twist-modifying systems (temperature, magnesium sulfate, and ammonium sulfate) revealed that changes in twist resulting from D-cycloserine were always in the opposite direction from those resulting from D-alanine. This antagonism suggests that the biochemical mechanism of twist regulation involves the metabolism of peptidoglycan, particularly reactions involving D-alanine or the dipeptide D-alanyl-D-alanine. This antagonism suggests that the biochemical mechanism of twist regulation involves the metabolism of peptidoglycan, particularly reactions involving D-alanine or the dipeptide D-alanyl-D-alanine. The possibility that peptidoglycan cross-linking is involved is discussed.     

Characterization of nutrition-induced helix hand inversion of Bacillus subtilis macrofibers.

The kinetics of Bacillus subtilis macrofiber helix hand inversion was examined. Inversion was induced by transfer of structures produced in one medium to another medium. When cultured at 20 degrees C in either medium, the doubling time was approximately 100 min. To establish a baseline, the macrofiber twist state produced in one medium was measured over the same time course during which other macrofibers underwent inversion after transfer to a second medium. The baseline was used to identify the time of inversion initiation: the point at which curves representing changes of twist as a function of time after transfer to the new medium intersected the baseline. Right- and left-handed macrofibers of different twists were produced by growth in mixtures of TB and S1 media. These were used to determine the influence of initial twist on the time course of inversion initiation. In the right to left inversion, a positive correlation was found between initial twist and the time of inversion initiation. The left to right inversion differed, however, in that a constant time was required for inversion initiation regardless of the starting left-handed twist. When a nutritional pulse was administered by transferring fibers from TB to S1 to TB medium, the time to initiation of inversion was found to decrease with incubation of increasing duration in S1 medium. A similar pulse protocol was used in conjunction with inhibitors to examine the protein and peptidoglycan synthesis requirements for the establishment of nutrition-induced memory that leads to initiation of inversion. Nutritionally induced right to left inversion but not left to right inversion required protein synthesis. The addition of trypsin to left-handed macrofibers apparently required, as described previously for the temperature-regulated twist system (D. Favre, D. Karamata, and N. H. Mendelson, J. Bacteriol. 164:1141-1145, 1985), for the production of left-handed twist states in the nutrition system.     

Regulation of Bacillus subtilis macrofiber twist development by ions: effects of magnesium and ammonium.

The steady-state twist of Bacillus subtilis macrofibers produced by growth in complex medium was found to vary as a function of the magnesium and ammonium concentrations. Four categories of macrofiber-producing strains that differed in their response to temperature regulation of twist were studied. Macrofibers were cultured in the complex medium TB used in previous experiments and in two derivative media, T (consisting of Bacto Tryptose), in which most strains produced left-handed structures, and Be (consisting of Bacto Beef Extract), in which right-handed macrofibers arose. In nearly all cases, increasing concentrations of magnesium led to the production of macrofibers with greater right-handed twist. Some strains unable to form right-handed structures as a function of temperature could be made to do so by the addition of magnesium. Inversion from right- to left-handedness in strain FJ7 induced by temperature shift-up was blocked by the addition of magnesium. The presence of magnesium during a high-temperature pulse did not block the establishment of "memory," although it delayed the initiation of the transient inversion following return to low temperature. The twist state of macrofibers grown without a magnesium supplement was not instantaneously affected by the addition of magnesium. Such fibers were, however, protected from lysozyme attack and associated relaxation motions. Lysozyme degradation of purified cell walls (both intact and lacking teichoic acid) was also blocked by the addition of magnesium. Ammonium ions influenced macrofiber twist development towards the left-hand end of the twist spectrum. Macrofiber twist produced in mixtures of magnesium and ammonium was strain and medium dependent.(ABSTRACT TRUNCATED AT 250 WORDS)     

Temperature-pulse-induced "memory" in Bacillus subtilis macrofibers and a role for protein(s) in the left-handed-twist state

Macrofibers in steady-state growth at one temperature were subjected to pulses of various durations at a temperature at which the opposite helix hand would form and then returned to the initial temperature. In an upshift pulse (20 to 48 degrees C), at least 3 min of incubation was required to induce a transient inversion that occurred later after return to 20 degrees C. Longer pulses resulted in shorter delays in onset of the transient inversion. This "memory" of a brief high-temperature pulse suggests that even a small amount of material can influence the twist of the entire macrofiber. Similar results were found for temperature downshift pulses corresponding to the opposite inversion. Adding chloramphenicol during the temperature pulse blocked the establishment of memory associated with the right-to-left inversion but not that associated with left-to-right inversion. In contrast, inhibiting peptidoglycan synthesis with D-cycloserine during the temperature pulse did not prevent establishment of memory. Inhibiting protein synthesis in mutants fixed as left-handed structures over the entire temperature range induced conversion to right-handedness but did not affect mutants fixed as right-handed structures. Adding protease to either live or formaldehyde-killed macrofibers always induced rotations of right-handed orientation. Steady-state growth in the presence of protease was found to shift the initial macrofiber twist towards the right-hand end of the twist spectrum. The phenomenon was observed in several mutants with different initial twists.     

Macrofiber structure and the dynamics of sickle cell hemoglobin crystallization

Fibers of deoxyhemoglobin S undergo spontaneous crystallization by a mechanism involving a variety of intermediate structures. These intermediate structures, in common with the fiber and crystal, consist of Wishner-Love double strands of hemoglobin S molecules arranged in different configurations. The structure of one of the key intermediates linking the fiber and crystal, called a macrofiber, has been studied by a variety of analytical procedures. The results of the analysis indicate that the intermediates involved in the fiber to crystal transition have many common structural features. Fourier analysis of electron micrographs of macrofibers confirms that they are composed of Wishner-Love double strands of hemoglobin molecules. Electron micrographs of macrofiber cross-sections reveal that the arrangement of the double strands in macrofibers resembles that seen in micrographs of the a axis projection of the crystal. This orientation provides an end-on view of the double strands which appear as paired dumb-bell-like masses. The structural detail becomes progressively less distinct towards the edge of the particle due to twisting of the double strands about the particle axis. Serial sections of macrofibers confirm that these particles do indeed rotate about their axes. The twist of the particle is right handed and its average pitch is 10,000 Å. The effect of rotation on the appearance of macrofiber cross-sections 300 to 400 Å thick can be simulated by a 15 ° rotation of an a axis crystal projection. The relative polarity of the double strands in macrofibers and crystals can be determined easily by direct inspection of the micrographs. In both macrofibers and crystals they are in an anti-parallel array.On the basis of these observations we conclude that crystallization of macrofibers involves untwisting and alignment of the double strands.     

Inversion of helix orientation in Bacillus subtilis macrofibers

The ability of helical macrofibers of Bacillus subtilis to convert from left- to right-handed structures or vice versa has been known to be controlled by the nutritional environment (N. H. Mendelson, Proc. Natl. Acad. Sci. U.S.A., 75:2478-2482, 1978). lyt mutants (Ni15, FJ3, FJ6, and FJ7) and also lyt phenocopies of wild-type strain FJ8 were able to undergo helix hand inversion as a function of temperature. The transition between right- and left-handed structures was in a very narrow range (about 2.5 degrees C) in the low to mid-40 degrees C. The helix orientation of these strains was also influenced by the concentration of divalent ions. Macrofiber handedness is governed, therefore, by at least four factors: genetic composition, temperature, and nutritional and ionic environments. Conditions normally used for growth fall, within this matrix, in the region favoring right-handed structures. Inhibition studies suggest that cell growth must occur for helix hand inversion.     

Dynamics of Bacillus subtilis helical macrofiber morphogenesis: writhing, folding, close packing, and contraction

Helical Bacillus subtilis macrofibers are highly ordered structures consisting of individual cells packed in a geometry remarkably similar to that found in helically twisted yarns (G. A. Carnaby, in J. W. S. Hearle et al., ed., The Mechanics of Flexible Fibre Assemblies, p. 99-112, 1980; N. H. Mendelson, Proc. Natl. Acad. Sci. U.S.A. 75:2478-2482, 1978). The growth and formation of macrofibers were studied with time-lapse microscopy methods. The basic growth mode consisted of fiber elongation, folding, and the helical wrapping together of the folded portion into a tight helical fiber. This sequence was reiterated at both ends of the structure, resulting in terminal loops. Macrofiber growth was accompanied by the helical turning of the structure along its long axis. Right-handed structures turned clockwise and left-handed ones turned counterclockwise when viewed along the length of a fiber looking toward a loop end. Helical turning forced the individual cellular filaments into a close-packing arrangement during growth. Tension was evident within the structures and they writhed as they elongated. Tension was relieved by folding, which occurred when writhing became so violent that the structure touched itself, forming a loop. When the multistranded structure produced by repeated folding cycles became too rigid for additional folding, the morphogenesis of a ball-like structure began. The dynamics of helical macrofiber formation was interpreted in terms of stress-strain deformations. In view of the similarities between macrofiber structures and those found in multifilament yarns and cables, the physics of helical macrofiber structure and also growth may be suitable for analysis developed in these fields concerning the mechanics of flexible fiber assemblies (C. P. Buckley; J. W. S. Hearle; and J. J. Thwaites, in J. W. S. Hearle et al., ed., The Mechanics of Flexible Fibre Assemblies, p. 1-97, 1980).     

Mechanics of bacterial macrofiber initiation.

The twisting and writhing during growth of single-cell filaments of Bacillus subtilis which lead to macrofiber formation was studied in both left- and right-handed forms of strains FJ7 and RHX. Filament bending, touching, and loop formation (folding), followed by winding up into a double-strand fiber, were documented. Subsequent folds that produced multistrandedness were also examined. The rate of loop rotation during winding up was measured for 26 loops from 16 clones. In most cases, the first loop formed turned at a lower rate than those produced by the following cycles of folding. The sequence of folding topologies differed in FJ7 and RHX strains and in left- versus right-handed structures. Right-handed FJ7 routinely gave rise to four-stranded helices at the second fold, whereas left-handed FJ7 and both left-handed and right-handed forms of RHX made structures with predominantly two double-stranded helical regions. Left-handed RHX structures frequently produced second folds within the initial loop itself, resulting in T- or Y-shaped fibers. Sixteen cases in which the initial touch of a filament to itself produced a loop that snapped open before it could wind up into a double-strand fiber were found. The snap motions were used to obtain estimates of the forces generated by helical growth of single filaments and to investigate theoretical models involving the material properties of cell filaments. In general, the mechanical behavior of growing single-cell filaments and fibers consisting of two-, three-, or four-strand helices was similar to that described for larger, mature, multifilament macrofibers. The behavior of multicellular macrofibers can be understood, therefore, in terms of individual cell growth.     

Clockwise and counterclockwise pinwheel colony morphologies of Bacillus subtilis are correlated with the helix hand of the strain

Helical macrofiber-producing strains of Bacillus subtilis grown on fresh complex medium semisolid surfaces formed "pinwheel"-shaped colonies. Clockwise pinwheel projections arose from colonies of strains that produce right-handed helical macrofibers in fluid cultures. Most strains able to make left-handed helical macrofibers in fluid grew as disorganized wavy colonies without directed projections. A phage-resistant left-handed mutant was found that produces very tight colonies with pinwheel projections that lie counterclockwise relative to the colony. The pinwheel colony morphology is interpreted therefore in terms of the cell surface organization and helical growth.     

Kinetic studies of temperature-induced helix hand inversion in Bacillus subtilis macrofibers.

The inversion of Bacillus subtilis macrofibers from right to left handedness induced by a temperature upshift was compared with inversion from left to right handedness induced by a temperature downshift. Following an upshift the new steady-state growth rate was achieved prior to inversion of helix orientation. There was no discernible perturbation of growth rate at the time of inversion. The time required after a temperature shift up or down for fiber rotation in the original sense to cease was dependent on the temperature to which the fibers were transferred and was always shortest when this temperature was highest. The results suggest a basic asymmetry in the two inversion processes. Cessation of rotation in the right-to-left inversion appeared to reflect contributions of the old and new wall materials that depended on their twist values, whereas the left-to-right inversion appeared to require that a specific amount of newly made wall material be inserted into the cell surface. The degree of twist of the newly inserted right-handed material appeared not to influence the timing of inversion.     

Identification of Mutations Associated with Macrofiber Formation in BACILLUS SUBTILIS

A search was made for the genes responsible for the production of helical macrofibers in the original collection of macrofiber-producing strains of B. subtilis. Two loci were identified: fibA, located between hisA and tag-1, and fibB, linked to cysB. fibA governs a short-lived division suppression phenomenon associated with the production of rudimentary fibers, whereas fibB appears to be responsible for a persistent division suppression and a more highly organized helical macrofiber. Both mutations are recovered from each of the original macrofiber-producing strains which also carried the div IV-B1 mutation responsible for minicell production. The latter mutation by itself is not sufficient, however, for the production of macrofibers. Other known mutations leading to division suppression that map in the same region are shown not to be allelic to fibA or fibB. Neither fib locus appears to be responsible for helix hand determination.     

Twist state phenotypes of Bacillus subtilis macrofibre mutants

The range of macrofibre twist states that can be achieved by various strains of Bacillus subtilis has been examined as a function of two variables: growth temperature and medium composition. Two graphic techniques were utilized to organize and compare data which pertain to the complex phenotypes of macrofibre mutants. The steady state twist states of strains were determined by qualitative examination. Structures were produced at each of the extremes of temperature and medium composition. Patterns obtained from a graphical representation of these data permitted the strains to be grouped into three classes: (A) strains in which helix-hand inversion could be triggered by nutrition at both 20 degrees or 48 degrees C, and by temperature in either medium; (B) strains in which a more limited set of conditions could induce inversion, and (C) strains which were restricted to either the right- or left-hand domain of twist states. Genetic factors governing these patterns were examined. Quantitative measurements of static twist were obtained over the entire temperature and media range, providing a detailed picture of the dependence of twist upon these environmental influences. Although the macrofibre twist state phenotype (as a function of both variables over the entire range of conditions) of each strain was unique, common features were discernible in all strains. Although some strains were limited to a single helix hand under all conditions studied, none were found to be restricted to a single twist state.     

Helix hand fidelity in Bacillus subtilis macrofibers after spheroplast regeneration.

Left- and right-handed Bacillus subtilis macrofibers produced by strains FJ7 and C6D were converted to spheroplasts. Intact cells were regenerated and macrofibers were produced under conditions conducive for production of left- and right-handed structures. The resulting helix hand phenotypes always corresponded to those expected on the basis of the parental genotype.     

Profilin is required for viral morphogenesis, syncytium formation, and cell-specific stress fiber induction by respiratory syncytial virus

Background

Bacterial macrofibers twist as they grow, writhe, supercoil and wind up into plectonemic structures (helical forms the individual filaments of which cannot be taken apart without unwinding) that eventually carry loops at both of their ends. Terminal loops rotate about the axis of a fiber's shaft in contrary directions at increasing rate as the shaft elongates. Theory suggests that rotation rates should vary linearly along the length of a fiber ranging from maxima at the loop ends to zero at an intermediate point. Blocking rotation at one end of a fiber should lead to a single gradient: zero at the blocked end to maximum at the free end. We tested this conclusion by measuring directly the rotation at various distances along fiber length from the blocked end. The movement of supercoils over a solid surface was also measured in tethered macrofibers.

Results

Macrofibers that hung down from a floating wire inserted through a terminal loop grew vertically and produced small plectonemic structures by supercoiling along their length. Using these as markers for shaft rotation we observed a uniform gradient of initial rotation rates with slopes of 25.6°/min. mm. and 36.2°/min. mm. in two different fibers. Measurements of the distal tip rotation in a third fiber as a function of length showed increases proportional to increases in length with constant of proportionality 79.2 rad/mm. Another fiber tethered to the floor grew horizontally with a length-doubling time of 74 min, made contact periodically with the floor and supercoiled repeatedly. The supercoils moved over the floor toward the tether at approximately 0.06 mm/min, 4 times faster than the fiber growth rate. Over a period of 800 minutes the fiber grew to 23 mm in length and was entirely retracted back to the tether by a process involving 29 supercoils.

Conclusions

The rate at which growing bacterial macrofibers rotated about the axis of the fiber shaft measured at various locations along fibers in structures prevented from rotating at one end reveal that the rate varied linearly from zero at the blocked end to maximum at the distal end. The increasing number of twisting cells in growing fibers caused the distal end to continuously rotate faster. When the free end was intermittently prevented from rotating a torque developed which was relieved by supercoiling. On a solid surface the supercoils moved toward the end permanently blocked from rotating as a result of supercoil rolling over the surface and the formation of new supercoils that reduced fiber length between the initial supercoil and the wire tether. All of the motions are ramifications of cell growth with twist and the highly ordered multicellular state of macrofibers.     

Rapid formation of tight junctions in HT 29 human adenocarcinoma cells by hypertonic salt solutions

The human colon adenocarcinoma cell line HT 29 grows virtually without tight junctions (TJ) under standard culture conditions. Earlier studies have shown that focal TJ (fasciae occludentes) can be rapidly assembled in this cell line under the influence of various proteases. Here we show that focal TJ can be induced in this cell line by a brief treatment with appropriate salt solutions. Induction by ammonium sulfate in Hanks' buffer reached a maximum value after 15 to 30 min. The amount of TJ increased with the salt concentration and reached a plateau value at a concentration of 160 mM ammonium sulfate. The amount and complexity of TJ induced by ammonium sulfate were similar to those in experiments using trypsin as inducing agent as shown by morphometric analysis. At 0 degrees C, no TJ were formed under the influence of the salt. A comparative study of TJ induction using a variety of inorganic and organic salts gave the following results. All alkali sulfates induced TJ, although with different yield. Both calcium and magnesium chloride were potent inducers. Ammonium and sodium salts encompassing a variety of anions covered a wide range from maximum induction (sulfate, citrate) to almost complete absence of induction (nitrate). Sodium chloride did not induce any TJ. It follows that the induction of TJ is a specific effect of individual ionic components of the solution as opposed to a general effect of osmolarity and ionic strength. The data suggest tentatively that antichaotropic but not chaotropic ions have the potential to trigger the formation of TJ in this experimental system.     

Description of the quaternary structure of tetrameric proteins. Forms that show either right-handed or left-handed symmetry at the subunit level.

A method is described for comparing the shapes of tetrameric proteins whose three-dimensional structure is known. The centres of mass of single subunits are calculated as Cartesian co-ordinates with respect to their three dyad axes. The axes are allocated on the basis of the extent of the intersubunit contacts that they relate. This results in the division of proteins into two classes called right-handed and left-handed. A second division, which also contains right-handed and left-handed forms, is made according to the distances between the centres of mass of the subunits measured across the two axes with the most extensive contacts. Two other parameters have been calculated from the coordinates; they are named "aplanarity" and "twist". The eight tetramers so far investigated are discussed. One, lactate dehydrogenase, cannot be treated in this way. Among the others, right-handed structures (according to both definitions) are found to be commoner; most have low twist; all are of fairly high aplanarity except phosphoglycerate mutase. Prealbumin is exceptional, being left-handed in both ways and of high twist; it has a figure-of-eight structure with the centres of mass lying in one plane. The changes in the quaternary structure of haemoglobin are also presented by using this approach; on deoxygenation the aplanarity and the twist decrease.     

Production of a new D-amino acid oxidase from the fungus Fusarium oxysporum.

The fungus Fusarium oxysporum produced a D-amino acid oxidase (EC 1. 4.3.3) in a medium containing glucose as the carbon and energy source and ammonium sulfate as the nitrogen source. The specific D-amino acid oxidase activity was increased up to 12.5-fold with various D-amino acids or their corresponding derivatives as inducers. The best inducers were D-alanine (2.7 microkat/g of dry biomass) and D-3-aminobutyric acid (2.6 microkat/g of dry biomass). The addition of zinc ions was necessary to permit the induction of peroxisomal D-amino acid oxidase. Bioreactor cultivations were performed on a 50-liter scale, yielding a volumetric D-amino acid oxidase activity of 17 microkat liter(-1) with D-alanine as an inducer. Under oxygen limitation, the volumetric activity was increased threefold to 54 microkat liter(-1) (3,240 U liter(-1)).     

Surprising Twists in Nucleosomal DNA with Implication for Higher-order Folding

While nucleosomes are dynamic entities that must undergo structural deformations to perform their functions, the general view from available high-resolution structures is a largely static one. Even though numerous examples of twist defects have been documented, the DNA wrapped around the histone core is generally thought to be overtwisted. Analysis of available high-resolution structures from the Protein Data Bank reveals a heterogeneous distribution of twist along the nucleosomal DNA, with clear patterns that are consistent with the literature, and a significant fraction of structures that are undertwisted. The subtle differences in nucleosomal DNA folding, which extend beyond twist, have implications for nucleosome disassembly and modeled higher-order structures. Simulations of oligonucleosome arrays built with undertwisted models behave very differently from those constructed from overtwisted models, in terms of compaction and inter-nucleosome contacts, introducing configurational changes equivalent to those associated with 2–3 base-pair changes in nucleosome spacing. Differences in the nucleosomal DNA pathway, which underlie the way that DNA enters and exits the nucleosome, give rise to different nucleosome-decorated minicircles and affect the topological mix of configurational states.     

Straightforward isolation of phosphatidyl-ethanolamine-binding protein-1 (PEBP-1) and ubiquitin from bovine testis by hydrophobic-interaction chromatography (HIC)

Isolation of phosphatidyl-ethanolamine-binding protein-1 (PEBP-1) from bovine brain was described almost three decades ago but it required a large number of steps to reach high purity. After the fractionation of bovine testis proteins by ammonium sulfate precipitation we found that PEBP-1, detected by Western blotting, was among the very few proteins still soluble at 80% ammonium sulfate saturation (3.2M). This soluble fraction (S80) was directly loaded onto a phenyl sepharose column equilibrated at the same ammonium sulfate concentration (3.2M). A stepwise elution of the retained material at 1.0, 0.5, 0.2, 0.1M ammonium sulfate in ammonium hydrogen carbonate was performed and then with ammonium hydrogen carbonate alone and finally with 50% ethylene glycol. All fractions were analyzed by SDS-PAGE and Western blotting and the fractions containing PEBP-1 was further fractionated by size exclusion chromatography on a HR75 Superdex column permitting the isolation of ubiquitin in addition to PEBP-1 as demonstrated by Western blotting and mass spectrometry. This study shows the feasibility of hydrophobic interaction chromatography (HIC) on phenyl sepharose at a very high ammonium sulfate concentration (3.2M; 80% saturation) to efficiently purify the proteins that are still soluble in these extreme conditions.     

Analysis of the peptidoglycan of Rickettsia prowazekii.

In the present study, peptidoglycan from Rickettsia prowazekii, an obligate intracellular bacterium, was purified. The rickettsial peptidoglycan is like that of gram-negative bacteria; that is, it is sodium dodecyl sulfate insoluble, lysozyme sensitive, and composed of glutamic acid, alanine, and diaminopimelic acid in a molar ratio of 1.0:2.3:1.0. The small amount of lysine found in the peptidoglycan preparation suggests that a peptidoglycan-linked lipoprotein(s) may be present in the rickettsiae. D-Cycloserine, a D-alanine analog which inhibits the biosynthesis of bacterial cell walls, prevented rickettsial growth in mouse L929 cells at a high concentration and altered the morphology of the rickettsiae at a low concentration. These effects were prevented by the addition of D-alanine. This suggests that R. prowazekii contains D-alanine in the peptidoglycan and has D-Ala-D-Ala ligase and alanine racemase activities.