Succinic semialdehyde couples stress response to quorum-sensing signal decay in Agrobacterium tumefaciens

Quorum sensing (QS) signal decay in Agrobacterium tumefaciens occurs in response to starvation or host signals. We have demonstrated that the gamma-aminobutyric acid (GABA) shunt metabolite links stress response to QS signal decay. Mutation of the aldH gene encoding a succinic semialdehyde dehydrogenase (SSADH) that converts succinic semialdehyde (SSA) to succinic acid results in early expression of the signal degrading enzyme, AttM. Exogenous addition of SSA or its precursor GABA induces AttM expression and abolishes Ti plasmid conjugative transfer. SSA acts by binding to the repressor AttJ that regulates the attKLM operon. attK encodes another SSADH. The stress alarmone ppGpp and SSA modulates separately the expression of the two SSADH enzymes, which might control the intracellular SSA level and hence to switch on/off the QS signal decay system in response to environmental changes. These findings document for the first time a sophisticated signalling mechanism of the widely conserved GABA degradation pathway in prokaryotes.     

The Ti plasmid of Agrobacterium tumefaciens harbors an attM-paralogous gene,aiiB, also encoding N-Acyl homoserine lactonase activity

The Agrobacterium tumefaciens C58 genome contains three putative N-acyl homoserine lactone (acyl-HSL) hydrolases, which are closely related to the lactonase AiiA of BACILLUS: When expressed in Escherichia coli, two of the putative acyl-HSL hydrolases, AttM and AiiB, conferred the ability to degrade acyl-HSLs on the host. In Erwinia strain 6276, the lactonases reduced the endogenous acyl-HSL level and the bacterial virulence in planta.     

Antigen secreted from noncytosolic Listeria monocytogenes is processed by the classical MHC class I processing pathway.

Intracellular bacteria can reside in a vacuolar compartment, or they can escape the vacuole and become free living in the cytoplasm. The presentation of Ag by class I MHC molecules has been defined primarily for Ag present in the cytoplasm. It was therefore thought that Ags from bacteria that remain in a vacuole would not be presented by MHC class I molecules. Although some studies have provided data to support this idea, it is not necessarily true for all intracellular bacteria. For example, we have previously demonstrated that an epitope from the p60 protein secreted by LLO- Listeria monocytogenes, which does not reside in the cytoplasm, can be presented by MHC class I molecules to a T cell clone specific for the epitope, p60217-225. We have further examined the route by which Ag secreted by LLO- L. monocytogenes is presented by MHC class I molecules. Using pharmacological inhibitors, we demonstrate that MHC class I presentation of the p60 epitope derived from by LLO- L. monocytogenes requires phagolysosome fusion and processing by the proteasome. Lysosomal cathepsins, however, are not required for processing of the p60 epitope. Similarly, processing of the AttM epitope, secreted by LLO- L. monocytogenes and presented by H2-M3, also requires phagolysosome fusion and cleavage by the proteasome. Thus, p60 and AttM secreted by LLO- L. monocytogenes are processed via the classical class I pathway for presentation by MHC class I molecules.     

Biocontrol of bacterial soft rot of calla lily by elicitor HarpinXoo and N-acyl homoserine lactonase (AttM)

Bacterial soft rot caused by Pectobacterium carotovorum subsp. carotovorum is a serious plant disease in Zantedeschia spp. (also called calla lily). In this study, two independent genes (a N-acyl homoserine lactonase gene attM from Agrobacterium tumefaciens and a hypersensitive response and pathogenicity gene hrf1 from Xanthomonas oryzae pv. oryzae), transcribed by a strong and constitutive Escherichia coli promoter P _lpp , respectively, were cloned into plasmid pUC19, and was transformed into E. coli, creating strain JM109/pPHA. The result of sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS–PAGE) assay showed that both genes (hrf1 and attM) were successfully expressed in one plasmid system in strain JM109/pPHA. The expressed Harpin_Xoo (Hrf1) and AttM protein had the ability of inducing hypersensitive response (HR) in nonhost tobacco and degrading the N-acyl homoserine lactones (AHLs) produced by P. carotovorum subsp. carotovorum, respectively, whereas Harpin_Xoo and AttM protein did not seem to interfere with the normal growth of this pathogen. In planta, strain JM109/pPHA could significantly reduce the soft rot disease severity on dormant tubers (control efficiency: 92.8%) or potted plants (control efficiency: 92.4%) of calla lily. We have first demonstrated the both biocontrol effects of Harpin_Xoo and AttM proteins (also described as Quorum interference) on the bacterial soft rot disease of calla lily, caused by P. carotovorum subsp. carotovorum. This work provided a potential way to control this serious plant disease.     

The Ti Plasmid of Agrobacterium tumefaciens Harbors an attM-Paralogous Gene, aiiB, Also Encoding N-Acyl Homoserine Lactonase Activity

The Agrobacterium tumefaciens C58 genome contains three putative N-acyl homoserine lactone (acyl-HSL) hydrolases, which are closely related to the lactonase AiiA of Bacillus. When expressed in Escherichia coli, two of the putative acyl-HSL hydrolases, AttM and AiiB, conferred the ability to degrade acyl-HSLs on the host. In Erwinia strain 6276, the lactonases reduced the endogenous acyl-HSL level and the bacterial virulence in planta.     

The BlcC (AttM) Lactonase of Agrobacterium tumefaciens Does Not Quench the Quorum-Sensing System That Regulates Ti Plasmid Conjugative Transfer

The conjugative transfer of Agrobacterium plasmids is controlled by a quorum-sensing system consisting of TraR and its acyl-homoserine lactone (HSL) ligand. The acyl-HSL is essential for the TraR-mediated activation of the Ti plasmid Tra genes. Strains A6 and C58 of Agrobacterium tumefaciens produce a lactonase, BlcC (AttM), that can degrade the quormone, leading some to conclude that the enzyme quenches the quorum-sensing system. We tested this hypothesis by examining the effects of the mutation, induction, or mutational derepression of blcC on the accumulation of acyl-HSL and on the conjugative competence of strain C58. The induction of blc resulted in an 8- to 10-fold decrease in levels of extracellular acyl-HSL but in only a twofold decrease in intracellular quormone levels, a measure of the amount of active intracellular TraR. The induction or mutational derepression of blc as well as a null mutation in blcC had no significant effect on the induction of or continued transfer of pTiC58 from donors in any stage of growth, including stationary phase. In matings performed in developing tumors, wild-type C58 transferred the Ti plasmid to recipients, yielding transconjugants by 14 to 21 days following infection. blcC-null donors yielded transconjugants 1 week earlier, but by the following week, transconjugants were recovered at numbers indistinguishable from those of the wild type. Donors mutationally derepressed for blcC yielded transconjugants in planta at numbers 10-fold lower than those for the wild type at weeks 2 and 3, but by week 4, the two donors showed no difference in recoverable transconjugants. We conclude that BlcC has no biologically significant effect on Ti plasmid transfer or its regulatory system.     

On the role,ecology, phylogeny,and structure of dual-family immunophilins

The novel class of dual-family immunophilins (henceforth abbreviated as DFI) represents naturally occurring chimera of classical FK506-binding protein (FKBP) and cyclophilin (CYN), connected by a flexible linker that may include a three-unit tetratricopeptide (TPR) repeat. Here, I report a comprehensive analysis of all current DFI sequences and their host organisms. DFIs are of two kinds: CFBP (cyclosporin- and FK506-binding protein) and FCBP (FK506- and cyclosporin-binding protein), found in eukaryotes. The CFBP type occurs in select bacteria that are mostly extremophiles, such as psychrophilic, thermophilic, halophilic, and sulfur-reducing. Essentially all DFI organisms are unicellular. I suggest that DFIs are specialized bifunctional chaperones that use their flexible interdomain linker to associate with large polypeptides or multisubunit megacomplexes to promote simultaneous folding or renaturation of two clients in proximity, essential in stressful and denaturing environments. Analysis of sequence homology and predicted 3D structures of the FKBP and CYN domains as well as the TPR linkers upheld the modular nature of the DFIs and revealed the uniqueness of their TPR domain. The CFBP and FCBP genes appear to have evolved in parallel pathways with no obvious single common ancestor. The occurrence of both types of DFI in multiple unrelated phylogenetic clades supported their selection in metabolic and environmental niche roles rather than a traditional taxonomic relationship. Nonetheless, organisms with these rare immunophilins may define an operational taxonomic unit (OTU) bound by the commonality of chaperone function.     

Apples, oranges, and the lunate sulcus

Holloway (1984) used a method of direct tape-arc measurements on chimpanzee brain casts to reject the hypothesis that the lunate sulcus is located in an anterior position in the Taung endocast. However, Holloway neglected to measure the occipital pole-lunate sulcus (OP-LS) arc directly on the Taung endocast as he did on chimpanzee brain casts (a crucial part of his methodology); instead, he determined the relative position of Taung's lunate sulcus on the basis of a calculation that confounds direct measurements and measurements from photographs. When arc OP-LS is measured directly on Taung according to Holloway's methods, the feature that has been identified as the medial end of the lunate sulcus is shown to be located within the range that Holloway determined for chimpanzees. Thus Holloway's methodology and data support rather than refute the claim that the lunate sulcus is located in a pongid-like position in australopithecines.     

Making Forest of Bliss: The Film, the Book, the DVD, and the Breakthrough

Robert Gardner's and Àkos Östör's Making of Forest of Bliss (2002) is a combination book and DVD that contains eight teaching tools for better understanding Gardner's celebrated film Forest of Bliss. After the film was shot in 1985, filmmaker Gardner and anthropologist Östör recorded a conversation about each image and sound of the film while they screened it again in 1987, and remembered their filmmaking process on location in Benares, India. The feature length (89 minute) documentary about death ritual, reincarnation, the sacred Ganges River, and the very atmosphere of Benares is included as DVD, as are teaching tools such as frame grabs (still images from the film), a mathematically precise shot list, bibliography, important criticism and essays about the film, and the featured in-depth conversation between filmmaker Gardner and anthropological advisor Östör. This essay articulates the unique breakthroughs in pedagogy, cross-cultural studies, and multidisciplinary analysis such hybrid technology provides.     

Development of the aphid parasitoid,Aphidius ervi, in asexual and sexual females of the pea aphid,Acyrthosiphon pisum, and the blackberry-cereal aphid,Sitobion fragariae

The aphid parasitoid,Aphidius ervi Haliday, overwinters in larval diapause. The possibility that the parasitoid might prefer sexual (oviparae) rather than asexual females (virginoparae) as overwintering hosts (oviparae predominate in autumn when host numbers are generally declining) was tested by comparing these aphid morphs as potential hosts. Two host species were also examined, the pea aphid,Acyrthosiphon pisum (Harris), and the blackberry aphid,Sitobion fragariae (Walker). The parasitoids took longer to develop inS. fragariae than inA. pisum but the development of non-diapausingA. ervi was similar in sexual and asexual females. This observation, together with the greater variation in the duration of the different parasitoid stadia inS. fragariae, indicated that the parasitoid is specialized on the pea aphid. In photophases of 12 h and longer, the proportion ofA. ervi entering diapause inA. pisum oviparae was higher than in virginoparae. The critical daylength (where 50% of parasitoids entered diapause) was therefore longer in oviparae (12.6 h) than in virginoparae (11.7 h) with the inference that parasitoids developing in the oviparae would enter diapause earlier in the field. InS. fragariae, critical day-lengths were similar in both aphid morphs. The duration of diapause was unaffected by host morph and emergence in short days (10:14 L:D) occurred over a long period (c. 60 days).     

Evaluation of the intramolecular stacking of the fluorosulfonylbenzoyl derivatives of 1,N6-ethenoadenosine, adenosine, and guanosine

The differences in conformation in solution of fluorosulfonylbenzoyl nucleosides were analyzed by fluorescence and proton nuclear magnetic resonance spectroscopy. The quantum yield of 5'-p-fluorosulfonylbenzoyl-1,N6-ethenoadenosine (5'-FSB epsilon A) in aqueous solution is low (? = 0.01) as compared to that of its parent nucleoside, ethenoadenosine (? = 0.54), and increases approximately 5-fold when measured in a series of solvents of decreasing dielectric constant. The quantum yield of 5'-p-sulfonylbenzoyl-1,N6-ethenoadenosine covalently bound to glutamate dehydrogenase and pyruvate kinase is also 0.01, suggesting that the analogue may exist in the same conformation when enzyme-bound as when free in solution. In D2O, the resonances of the purine ring protons on 5'-FSB epsilon A, 5'-p-fluorosulfonylbenzoyl adenosine (5'-FSBA), and 5'-p-fluorosulfonylbenzoyl guanosine (5'-FSBG) are shifted upfield by about 0.1-0.3 ppm relative to the corresponding protons of their parent nucleosides. The calculated difference in chemical shift (delta delta) decreases as the dielectric constant of the solvent decreases. The delta delta decreases with increasing temperature. These data indicate that 5'-FSB epsilon A, 5'-FSBA, and 5'-FSBG exist in aqueous solution in a conformation in which the purine ring is intramolecularly stacked with the benzoyl moiety. From the magnitude of change in delta delta for 5'-FSB epsilon A, 5'-FSBA, and 5'-FSBG as a function of solvent, it appears that the three analogues differ in their sensitivity to disruption of stacking. The solution conformation of these three fluorosulfonylbenzoyl nucleoside analogues may be an important determinant of their reaction with various enzymes and may explain differences among the analogues in their reaction with a single enzyme.     

Bonding, biophilia, biosynergy, and the future of primates in the wild

Human and nonhuman primates bond with one another in countless ways, and the results are varied and vital to the individuals and species involved. The manifesto that is the basis for the collection of essays in which this commentary is included proposes that the "human/nonhuman bonds that arise in primatological research and practice deserve and demand study and research." An essential corollary of this proposal is that the primatologists themselves must be studied. The aim of this essay is to explore the influence of human/nonhuman primate bonding on conservation practice and on the future of primates in the wild. This commentary applies the author's professional experience as a conservation psychologist and his research on the impact of profound interspecies bonds on human worldviews, attitudes, and behavior. It examines two general categories of bonds: those driven by Biophilia (human fascination with life) and those influenced by Biosynergy (mutual enrichment of life). It is the author's premise that biosynergy promotes complex collaborative interspecies bonds that broaden the conservationist's desire to enhance synergy among all organisms in an ecosystem. Conversely, biophilia induces relatively simple unidirectional bonds between humans and other animals that deepen the conservationist's desire to understand and protect certain species. This contrast raises some crucial questions. Do biophilia-driven bonds between conservationists and their favorite primates blind them to the synergistic needs of all species and impair their ability to work for sustained preservation of threatened habitat? Does biosynergy-based human/nature bonding enhance focus on conservation as an ecological science and thus ignore species-specific factors crucial to assure survival of endangered primates? How can both types of bonds be optimally applied to the conservation of wildlife and wilderness?     

Localization of the Lys, Asp, Glu, Leu tetrapeptide receptor to the Golgi complex and the intermediate compartment in mammalian cells

The carboxyl-terminal Lys-Asp-Glu-Leu (KDEL), or a closely-related sequence, is important for ER localization of both lumenal as well as type II membrane proteins. This sequence functions as a retrieval signal at post-ER compartment(s), but the exact compartment(s) where the retrieval occurs remains unresolved. With an affinity-purified antibody against the carboxyl-terminal sequence of the mammalian KDEL receptor, we have investigated its subcellular localization using immunogold labeling on thawed cryosections of different tissues, such as mouse spermatids and rat pancreas, as well as HeLa, Vero, NRK, and mouse L cells. We show that rab1 is an excellent marker of the intermediate compartment, and we use this marker, as well as budding profiles of the mouse hepatitis virus (MHV) in cells infected with this virus, to identify this compartment. Our results demonstrate that the KDEL receptor is concentrated in the intermediate compartment, as well as in the Golgi stack. Lower but significant labeling was detected in the rough ER. In general, only small amounts of the receptor were detected on the trans side of the Golgi stack, including the trans- Golgi network (TGN) of normal cells and tissues. However, some stress conditions, such as infection with vaccinia virus or vesicular stomatitis virus, as well as 20 degrees C or 43 degrees C treatment, resulted in a significant shift of the distribution towards the trans- TGN side of the Golgi stack. This shift could be quantified in HeLa cells stably expressing a TGN marker. No significant labeling was detected in structures distal to the TGN under all conditions tested. After GTP gamma S treatment of permeabilized cells, the receptor was detected in the beta-COP-containing buds/vesicles that accumulate after this treatment, suggesting that these vesicles may transport the receptor between compartments. We propose that retrieval of KDEL- containing proteins occurs at multiple post-ER compartments up to the TGN along the exocytotic pathway, and that within this pathway, the amounts of the receptor in different compartments varies according to physiological conditions.     

Psychophysics, intensive magnitudes, and the psychometricians' fallacy

As an aspiring science in the nineteenth and early twentieth centuries, psychology pursued quantification. A problem was that degrees of psychological attributes (most importantly, then, intensities of sensations) were experienced only as greater than, less than, or equal to one another. They were categorised as intensive magnitudes. The meaning of this concept was shifting, from that of an attribute possessing underlying quantitative structure (the medieval and Kantian meaning) to that of a merely ordinal attribute (its dominant twentieth-century meaning). This fluidity allowed psychologists to claim that their attributes were intensive magnitudes (because ordered) and measurable (because intensive magnitudes). This claim was supported by an argument that order entails quantity. As adapted by psychometricians, the argument was that if an attribute is ordered, then the differences between its degrees are quantitative and, therefore, measurable. However, in a paper ignored in psychology for six decades, the issue was resolved mathematically and the resolution implies that the psychometricians' argument was fallacious.     

Sugar,fat, and the risk of colorectal cancer.

The habitual diet of 50 patients with large bowel cancer, as assessed by a dietary history method, was compared with that of 50 closely matched controls. Patients were included only if their symptoms were unlikely to have changed previous eating habits. The mean daily intakes of all major nutrient classes and of dietary fibre were estimated. Patients with large bowel cancer consumed 16% more energy than controls (mean (SEM) daily intake 9.92 (0.41) v 8.56 (0.32) MJ (2370 (98) v 2046 (76) kcal), respectively; p less than 0.0001), mainly in the form of carbohydrate (21% more; 282.6 (13.7) v 233.4 (10.5) g; p less than 0.0001) and fat (14% more; 100.8 (4.3) v 88.4 (3.2) g; p less than 0.001). The extra carbohydrate was largely in the form of sugars depleted in fibre and the extra fat as combinations of fat and such sugars. As the selection criteria used make it unlikely that this eating pattern was caused by the disease the data suggest that a high intake of sugars depleted in fibre and fat predisposes to the development of large bowel cancer.     

Tunicate tails, stolons, and the origin of the vertebrate trunk

Tunicates are primitive chordates that develop a transient 'tail' in the larval stage that is generally interpreted as a rudimentary version of the vertebrate trunk. Not all tunicates have tails, however. The groups that lack them, salps and pyrosomes, instead have a trunk-like reproductive stolon located approximately where the tail would otherwise be. In salps, files of blastozooids are formed along the sides of the stolon. The tail and caudal trunk in more advanced chordates could have evolved from a stolon of this type, an idea referred to here as the 'stolon hypothesis'. This means the vertebrate body could be a composite structure, since there is the potential for each somite to incorporate elements originally derived from a complete functional zooid. If indeed this has occurred, it should be reflected in some fashion in gene expression patterns in the vertebrate trunk. Selected morphological and molecular data are reviewed to show that they provide some circumstantial support for the stolon hypothesis. The case would be stronger if it could be demonstrated that salps and/or pyrosomes are ancestral to other tunicates. The molecular phylogenies so far available generally support the idea of a pelagic ancestor, but offer only limited guidance as to which of the surviving pelagic groups most closely resembles it. The principal testable prediction of the stolon hypothesis is that head structures (or their homologues) should be duplicated in series in the trunk in advanced chordates, and vice versa, i.e. trunk structures should occur in the head. The distribution of both rhabdomeric photoreceptors and nephridia in amphioxus conform with this prediction. Equally striking is the involvement of the Pax2 gene in the development of both the inner ear and nephric ducts in vertebrates. The stolon hypothesis would explain this as a consequence of the common origin of otic capsules and excretory ducts from atrial rudiments: from the paired rudiments of the parent oozooid in the case of the otic capsule (these express Pax2 according to recent ascidian data), and from tubular rudiments in the stolon in the case of the excretory ducts.     

Phylogeny, regression, and the allometry of physiological traits

Physiological and ecological allometries often pose linear regression problems characterized by (1) noncausal, phylogenetically autocorrelated independent (x) and dependent (y) variables (characters); (2) random variation in both variables; and (3) a focus on regression slopes (allometric exponents). Remedies for the phylogenetic autocorrelation of species values (phylogenetically independent contrasts) and variance structure of the data (reduced major axis [RMA] regression) have been developed, but most functional allometries are reported as ordinary least squares (OLS) regression without use of phylogenetically independent contrasts. We simulated Brownian diffusive evolution of functionally related characters and examined the importance of regression methodologies and phylogenetic contrasts in estimating regression slopes for phylogenetically constrained data. Simulations showed that both OLS and RMA regressions exhibit serious bias in estimated regression slopes under different circumstances but that a modified orthogonal (least squares variance-oriented residual [LSVOR]) regression was less biased than either OLS or RMA regressions. For strongly phylogenetically structured data, failure to use phylogenetic contrasts as regression data resulted in overestimation of the strength of the regression relationship and a significant increase in the variance of the slope estimate. Censoring of data sets by simulated extinction of taxa did not affect the importance of appropriate regression models or the use of phylogenetic contrasts.