Structure of bacterial cytoplasmic chemoreceptor arrays and implications for chemotactic signaling

Most motile bacteria sense and respond to their environment through a transmembrane chemoreceptor array whose structure and function have been well-studied, but many species also contain an additional cluster of chemoreceptors in their cytoplasm. Although the cytoplasmic cluster is essential for normal chemotaxis in some organisms, its structure and function remain unknown. Here we use electron cryotomography to image the cytoplasmic chemoreceptor cluster in Rhodobacter sphaeroides and Vibrio cholerae. We show that just like transmembrane arrays, cytoplasmic clusters contain trimers-of-receptor-dimers organized in 12-nm hexagonal arrays. In contrast to transmembrane arrays, however, cytoplasmic clusters comprise two CheA/CheW baseplates sandwiching two opposed receptor arrays. We further show that cytoplasmic fragments of normally transmembrane E. coli chemoreceptors form similar sandwiched structures in the presence of molecular crowding agents. Together these results suggest that the 12-nm hexagonal architecture is fundamentally important and that sandwiching and crowding can replace the stabilizing effect of the membrane.

DOI:http://dx.doi.org/10.7554/eLife.02151.001

Many bacteria swim through water by rotating tiny hair-like structures called flagella. In E. coli, if all the flagella on the surface of a bacterium rotate in a counterclockwise fashion, then it will swim in a particular direction, but if the flagella all rotate in an clockwise fashion, then the bacterium will stop swimming and start to tumble.

Bacteria use a combination of swimming and tumbling in order to move towards or away from certain chemicals. For example, a bacterium is able to move towards a source of nutrients because it is constantly evaluating its environment and will swim forward for longer periods of time when it recognizes the concentration of the nutrient is increasing. And if it senses that the nutrient concentration is decreasing, it will tumble in an effort to move in a different direction.

Many bacteria, such as E. coli, rely on proteins in their cell membrane called chemoreceptors to sense specific chemicals and then send signals that tell the flagella how to rotate. These transmembrane receptors and their role in chemotaxis—that is, movement towards or away from specific chemicals in the environment—have been widely studied. However, other bacteria also have chemoreceptors in the cytoplasm inside the bacterial cell, and much less is known about these.

Now, Briegel et al. have examined the cytoplasmic chemoreceptors of two unrelated bacteria, R. sphaeroides and V. cholera, and found that the cytoplasmic chemoreceptors arrange themselves in hexagonal arrays, similar to the way that transmembrane chemoreceptors are arranged. However, the cytoplasmic chemoreceptors arrange themselves in a two-layer sandwich-like structure, whereas the transmembrane chemoreceptors are arranged in just one layer. The next step is to understand how chemical binding causes these arrays to send their signals to the motor. A complete understanding of this signaling system may ultimately allow scientists to re-engineer it to draw bacteria to targets of medical or environmental interest, such as cancer cells or contaminated soils.

DOI:http://dx.doi.org/10.7554/eLife.02151.002

New insights into bacterial chemoreceptor array structure and assembly from electron cryotomography

Bacterial chemoreceptors cluster in highly ordered, cooperative, extended arrays with a conserved architecture, but the principles that govern array assembly remain unclear. Here we show images of cellular arrays as well as selected chemoreceptor complexes reconstituted in vitro that reveal new principles of array structure and assembly. First, in every case, receptors clustered in a trimers-of-dimers configuration, suggesting this is a highly favored fundamental building block. Second, these trimers-of-receptor dimers exhibited great versatility in the kinds of contacts they formed with each other and with other components of the signaling pathway, although only one architectural type occurred in native arrays. Third, the membrane, while it likely accelerates the formation of arrays, was neither necessary nor sufficient for lattice formation. Molecular crowding substituted for the stabilizing effect of the membrane and allowed cytoplasmic receptor fragments to form sandwiched lattices that strongly resemble the cytoplasmic chemoreceptor arrays found in some bacterial species. Finally, the effective determinant of array structure seemed to be CheA and CheW, which formed a "superlattice" of alternating CheA-filled and CheA-empty rings that linked receptor trimers-of-dimer units into their native hexagonal lattice. While concomitant overexpression of receptors, CheA, and CheW yielded arrays with native spacing, the CheA occupancy was lower and less ordered, suggesting that temporal and spatial coordination of gene expression driven by a single transcription factor may be vital for full order, or that array overgrowth may trigger a disassembly process. The results described here provide new insights into the assembly intermediates and assembly mechanism of this massive macromolecular complex.

Heat management strategies for solid-state NMR of functional proteins

Modern solid-state NMR methods can acquire high-resolution protein spectra for structure determination. However, these methods use rapid sample spinning and intense decoupling fields that can heat and denature the protein being studied. Here we present a strategy to avoid destroying valuable samples. We advocate first creating a sacrificial sample, which contains unlabeled protein (or no protein) in buffer conditions similar to the intended sample. This sample is then doped with the chemical shift thermometer Sm2Sn2O7. We introduce a pulse scheme called TCUP (for Temperature Calibration Under Pulseload) that can characterize the heating of this sacrificial sample rapidly, under a variety of experimental conditions, and with high temporal resolution. Sample heating is discussed with respect to different instrumental variables such as spinning speed, decoupling strength and duration, and cooling gas flow rate. The effects of different sample preparation variables are also discussed, including ionic strength, the inclusion of cryoprotectants, and the physical state of the sample (i.e. liquid, solid, or slurry). Lastly, we discuss probe detuning as a measure of sample thawing that does not require retuning the probe or using chemical shift thermometer compounds. Use of detuning tests and chemical shift thermometers with representative sample conditions makes it possible to maximize the efficiency of the NMR experiment while retaining a functional sample.

3D Reconstruction of a Subcomplex of NADH-ubiquinone-oxidoreductase (Complex I) from Yarrowia lipolytica

Extended abstract of a paper presented at Microscopy and Microanalysis 2011 in Nashville, Tennessee, USA, August 7–August 11, 2011.

Design and characterization of a calixarene inclusion compound for calibration of long-range carbon-fluorine distance measurements by solid-state NMR

An inexpensive, easily synthesized calixarene:fluorotoluene host:guest inclusion complex has been designed for optimization and calibration of solid-state NMR measurements of carbon-fluorine distances using Rotational Echo DOuble Resonance (REDOR). Complexation of the fluorotoluene with the calixarene host separates the molecules such that simple two-spin behavior is observed for one site with a 4.08 Å carbon-fluorine distance. Fluorotoluene dynamics within the calixarene matrix cause motional averaging of the dipolar couplings, which makes it possible to easily optimize REDOR experiments and test their accuracy for relatively long distance measurements (>6.6 Å). This provides a new tool for accurate REDOR measurements of long carbon-fluorine distances, which have important applications in the characterization of fluorine-containing drugs, proteins, and polymers.

Kinase-active signaling complexes of bacterial chemoreceptors do not contain proposed receptor-receptor contacts observed in crystal structures

The receptor dimers that mediate bacterial chemotaxis form high-order signaling complexes with CheW and the kinase CheA. From the packing arrangement in two crystal structures of different receptor cytoplasmic fragments, two different models have been proposed for receptor signaling arrays: the trimers-of-dimers and hedgerow models. Here we identified an interdimer distance that differs substantially in the two models, labeled the atoms defining this distance through isotopic enrichment, and measured it with (19)F-(13)C REDOR. This was done in two types of receptor samples: isolated bacterial membranes containing overexpressed, intact receptor and soluble receptor fragments reconstituted into kinase-active signaling complexes. In both cases, the distance found was not compatible with the receptor dimer-dimer contacts observed in the trimers-of-dimers or in the hedgerow models. Comparisons of simulated and observed REDOR dephasing were used to deduce a closest approach distance at this interface, which provides a constraint for the possible arrangements of receptor assemblies.

Electron Microscopy of Chorionic Villus Samples for Prenatal Diagnosis of Lysosomal Storage Disorders

Some lysosomal storage disorders cause progressive prenatal accumulation of undegradable metabolites that manifest as membrane-bound vacuoles in endothelial cells, fibroblasts, and trophoblast, identifiable by electron microscopic examination of chorionic villus samples (CVS). There were 111 CVS, which had ultrastructural examination for suspected storage disorders at Great Ormond Street Hospital (1988-2005). There were 31 positive diagnoses, including glycogen storage disease type II, gangliosidosis type 1, mucopolysaccharidosis type 1, MPS not specified, Niemann-Pick type A, sialidosis/mucolipidosis type 1, neuronal ceroid lipofuscinoses (including variant forms), Wolman disease, sialic acid storage disease, and storage disease not specified. In most of these cases the indication was a previously affected individual. Seventy-seven cases showed no evidence of storage disease; 3 samples were inadequate for ultrastructural diagnosis. In selected cases, one-third of CVS may demonstrate distinctive ultrastructural features allowing prenatal diagnosis of a range of storage diseases.

Histomorphometric features of hydatidiform moles in early pregnancy: relationship to detectability by ultrasound examination

OBJECTIVE

The majority of partial (PHM) and complete (CHM) hydatidiform moles are diagnosed in early pregnancy. About half are identified as molar on ultrasonographic examination prior to evacuation. It is uncertain whether unsuspected cases represent an intrinsically different molar phenotype or are simply dependant on sonographer expertise. We measured a microscopic parameter, average villus diameter, of evacuated PHMs and CHMs to ascertain the cause of non-detection on ultrasound.

METHODS

Fifty-four molar pregnancies were examined from the files of the Trophoblastic Disease Unit, in which results of an ultrasound examination prior to evacuation were known. In each, the average cross-sectional diameter of the largest 10 villi was recorded. Maximum villus diameters were compared between gestational age groups (<14 weeks and >or=14 weeks), and ultrasound detection groups (detected (d) and not detected (nd)).

RESULTS

The average maximum villus diameter of the largest hydropic villi was significantly less in the first trimester for both PHMs and CHMs that were undetected by ultrasound examination compared to those identified as molar sonographically (P<0.001 and P<0.001, respectively). There was no significant difference in the maximum villus diameter between PHMs and CHMs that were not detected sonographically in the first trimester (P=0.44). Beyond 14 weeks of gestation, there was no significant difference between PHMs detected and undetected sonographically (P=0.88).

CONCLUSION

The average diameter of the largest, most hydropic villi, is significantly greater in cases of PHMs and CHMs detected by ultrasound examination in the first trimester compared to that of those not detected sonographically, but beyond 14 weeks such differences are minimal. These findings suggest that, although sonographer expertise could potentially increase ultrasound detection rates somewhat for PHMs and CHMs, a significant proportion of cases demonstrate minimal hydropic change in the first trimester and are therefore likely to remain unidentifiable by ultrasound examination prior to evacuation, even with improved sonographer expertise.

Ultrastructural features of gaucher disease treated with enzyme replacement therapy presenting as mesenteric mass lesions

The classical ultrastructural features of Gaucher disease include large numbers of intracytoplasmic, membrane-bound lysosomal inclusions containing characteristic tubular structures on an electron-lucent background, representing the periodic acid schiff (PAS)-positive Gaucher cells identifiable on light microscopy. Following enzyme replacement therapy (ERT), many of the manifestations of the condition are ameliorated, but persistent mesenteric lymphadenopathy has been reported, the ultrastructural features of which previously have not been described. Two children, aged 4 and 8 years old, respectively, both presented with persistent abdominal lymphadenopathy whilst receiving ERT for Gaucher disease. Needle core biopsies were carried out, that demonstrated collections of macrophages and only scattered storage-type cells on light microscopy. PAS staining was negative in one case and only focally positive in the other Electron microscopic examination, however, confirmed the cells represented macrophages, the cytoplasm of which contained scattered abnormal inclusions containing occasional twisted tubular structures of the type reported in classic Gaucher disease. ERT in Gaucher disease appears to reduce accumulation of the metabolic products at many sites. But for uncertain reasons, abdominal lymphadenopathy may occur containing macrophages that do not form granulomas or classic Gaucher cells on light microscopy. These probably represent incomplete clearance, incomplete/partial enzyme replacement, or possibly an unusual response to a relatively small amount of storage material.

Primary thoracic myxoid variant of extrarenal rhabdoid tumor in childhood

Primary extrarenal rhabdoid tumors (RT) are now recognized as a specific entity in pediatric oncological pathology practice. We present an unusual case of a small cell myxoid variant of a thoracic RT in an infant and highlight the importance of recent molecular developments in the diagnosis of these tumors. An 8-month-old child presented with a short history of cough and shortness of breath. Imaging demonstrated a large mass occupying the majority of the thoracic cavity on the right side. A percutaneous needle biopsy of the mass showed fragments of tissue composed of malignant tumor with a predominant "small ovoid cell" phenotype and extensive myxoid change, with small nests and islands of tumor cells; occasional cells demonstrated open vesicular nuclei, prominent nucleoli, and eosinophilic cytoplasmic inclusions. Immunohistochemical staining revealed focal strong cytoplasmic positivity for cytokeratin, focal strong paranuclear cytoplasmic vimentin positivity, and INI1 staining showed normal nuclear positivity in control tissues but was negative in tumor cell nuclei. Electron microscopy demonstrated characteristic paranuclear whorls of intermediate filaments confirming the diagnosis of extrarenal malignant RT. The diagnosis of malignant rhabdoid tumor may be difficult, particularly in cases, such as the present, with a predominant small-cell myxoid phenotype. The characteristic expression patterns of cytokeratin and vimentin provide strong clues to the diagnosis, and the use of INI1 antibody now makes definitive diagnosis possible even on needle core biopsies.

Evidence for the Role of the monB Genes in Polyether Ring Formation during Monensin Biosynthesis

Ionophoric polyethers are produced by the exquisitely stereoselective oxidative cyclization of a linear polyketide, probably via a triepoxide intermediate. We report here that deletion of either or both of the monBI and monBII genes from the monensin biosynthetic gene cluster gave strains that produced, in place of monensins A and B, a mixture of C-3-demethylmonensins and a number of minor components, including C-9-epi-monensin A. All the minor components were efficiently converted into monensins by subsequent acid treatment. These data strongly suggest that epoxide ring opening and concomitant polyether ring formation are catalyzed by the MonB enzymes, rather than by the enzyme MonCII as previously thought. Consistent with this, homology modeling shows that the structure of MonB-type enzymes closely resembles the recently determined structure of limonene-1,2-epoxide hydrolase from Rhodococcus erythropolis.

Melanotic neuroectodermal tumor of infancy: clinical, radiological, and pathological features

We present a case of a 4-month-old female infant with a maxillary melanotic neuroectodermal tumor of infancy (MNTI) and review the pooled data from previous publications on this entity. The literature to date comprises 378 reported cases from 1918 to the present, from which data on the presence or absence of metastatic disease was available in 311, and on the presence or absence of local recurrence in 165. These pooled data suggest a local recurrence rate of 36% with metastasis occurring in 7% of cases. At present, the optimal management includes complete surgical excision with clear margins, but there are no reliable histopathological or molecular features to predict the biological behavior in individual cases.

Routine pre-evacuation ultrasound diagnosis of hydatidiform mole: experience of more than 1000 cases from a regional referral center

OBJECTIVES

To examine the accuracy of sonographic findings of routine ultrasound examinations in patients with a proven histological diagnosis of complete or partial hydatidiform mole referred to a supra-regional referral center, and to examine the relationship of sonographic findings to gestational age across the first and early second trimesters.

METHODS

Review of consecutive cases referred to a trophoblastic disease unit from June 2002 to January 2005 with a diagnosis of possible or probable hydatidiform mole in whom results of a pre-evacuation ultrasound examination were documented. Ultrasound detection rates for partial and complete hydatidiform moles were calculated and comparison of detection rates between complete and partial mole, and gestational age groups carried out.

RESULTS

1053 consecutive cases were examined. The median maternal age was 31 (range, 15-54) years and the median gestational age was 10 (range, 5-27) weeks. 859 had a final review diagnosis of partial or complete hydatidiform mole (82%), including 253 (29%) complete moles and 606 (71%) partial moles. Non-molar hydropic miscarriage was diagnosed following histological review in 194 (18%). Overall, 378 (44%) cases with a final diagnosis of complete or partial hydatidiform mole had a pre-evacuation ultrasound diagnosis suggesting hydatidiform mole, including 200 complete moles and 178 partial moles, representing 79% and 29%, respectively, of those with complete (253) or partial (606) moles in the final review diagnosis. The ultrasound detection rate was significantly better for complete versus partial hydatidiform moles (Z = 13.4, P < 0.001). There was a non-significant trend towards improved ultrasound detection rate with increasing gestational age, with an overall detection rate of 35-40% before 14 weeks' gestation compared to around 60% after this gestation. The sensitivity, specificity, positive predictive value and negative predictive value for routine pre-evacuation ultrasound examination for detection of hydatidiform mole of any type were 44%, 74%, 88% and 23%, respectively.

CONCLUSIONS

Routine pre-evacuation ultrasound examination identifies less than 50% of hydatidiform moles, the majority sonographically appearing as missed or incomplete miscarriage. Detection rates are, however, higher for complete compared to partial moles, and improve after 14 weeks' gestation. Histopathological examination of products of conception remains the current gold standard for the identification of gestational trophoblastic neoplasia.

Synthesis of C-linked glycopyranosyl serines via a chiral glycine enolate equivalent

[formula: see text] The stereoselective preparation of C-linked D-gluco- and D-galactopyranosyl L-serines in their alpha and beta forms is herein reported. The syntheses require the conversion of the allyl C-glycopyranosides into their iodoethyl derivatives, which then undergo substitution with the Williams' chiral glycine enolate equivalent. Deprotection and acetylation affords Boc-protected amino acids for peptide synthesis.

Prenatal diagnosis and molecular cytogenetics in a case of partial trisomy 14 and monosomy 21

We report an unbalanced translocation involving chromosomes 14 and 21 which presented as fetal ventriculomegaly at 33 weeks gestation. Second trimester ultrasound had indicated normal fetal anatomy, including normal intracranial structures. Parental karyotypes showed a paternal balanced translocation: 46,XY,t(14;21)(q12;q21). The unbalanced translocation in the fetus resulted in trisomy for 14pter-->q12 and monosomy for 21pter-->q21. Postnatal examination showed that the male infant had a cleft palate, but no cleft lip, and mild dysmorphic features. Postnatal MRI revealed bilateral and symmetric dilatation of the occipital horns, atria, and temporal horns of the lateral ventricles. Molecular cytogenetic techniques were used to delineate further the breakpoint on chromosome 14 to a site distal of the D14S1071 locus and the breakpoint on chromosome 21 to a region between D21S1918 and D21S1902. More precise definitions of chromosomal breakpoints in such clinical cases should provide more accurate prognosis for individuals with unbalanced karyotypes and assist in the identification of putative developmentally important genes.

Insulin-like growth factor binding protein-1 (IGFBP-1): a multifunctional role in the human female reproductive tract

Insulin-like growth factor-1 (IGFBP-1) is particularly important in human female reproductive physiology, where it is involved with other factors in a complex system which regulates menstrual cycles, puberty, ovulation, decidualization, implantation and fetal growth. This has implications for clinical obstetrics and gynaecology, where there is evidence for a pathophysiological role for IGFBP-1 in pre-eclampsia, intrauterine growth restriction, polycystic ovarian syndrome and trophoblast and endometrial neoplasms.

The interrelationships between serotonin production and locomotion in different light regimes in southwestern Michigan opilionids, Leiobunum longipes

The comparison was made of the effect of LL and DD with LD 14:10 photoperiods on the 24-h secretion cycle of serotonin secretion and the activity patterns of Leiobunum longipes from Southwestern Michigan. LL and DD altered the normal activity patterns but did not change the pattern of serotonin secretion. The activity pattern in normal photoperiod (LD 14:10) produced a 12-h cosinor pattern, resulting in a 24-h biphasic activity peak model. The activity peaked in both scotophase and photophase . The altered patterns in LL and DD were different. In LL a rhythmic component could not be statistically determined. A high, irregular level of activity was seen, higher than the mean level in LD. In DD a combined 24 and 48 h cosinor pattern best fit the observed data. The major peaks occurred in nature during every other photophase and alternate scotophase time in the constant photoperiod conditions. Serotonin secretion patterns in LD, LL, and DD statistically fitted a 24-h cosinor model. Peak secretion times occurred in mid photophase for LD and LL. A later photophase peak was seen in DD. LL animals showed a mean level of serotonin and secretion pattern which was not statistically different from LD. The hypothesis that LD photoperiods direct a peak of serotonin secretion which initiated the activity pattern could not be accepted.

Neurosecretory cells: daily rhythmicity in Leiobunum longipes

A fluorometric-analysis procedure, used to quantitate indoles, confirmed the presence of 5-hydroxytryptamine (5-HT) in an arachnid; there was unimodal cyclic production of 5-HT in brain and intestinal tissues over a 24-hour period. The same tissues produced 5-HT after 80-day culture; bimodal cyclic output was indicated during continuous 24-hour study. One peak occurred at 0200 hours, at the same time as the peak in vivo, suggesting an endogenously controlled mechanism of secretion. The second peak occurred at midmorning, a time when production in vivo was lowest, suggesting that there is a possible feedback-control mechanism in the organism that inhibits the endogenous output of 5-HT.