The consequences of volatile organic compound mediated bacterial and fungal interactions

Microbial interactions via infochemicals are fundamental to the development of spatial distribution and activity variations in ecosystems. Microorganisms produce a wide range of infochemicals, frequently secondary metabolites, most of which are soluble and many volatile. Volatile organic compounds (VOCs) have been identified in soil atmospheres and related to community structure and function. VOC profiles produced by microorganisms are consistent, relating to cultural conditions, environment and inputs, and so to population and function dynamics. VOC-mediated interactions can result in functional responses by the organisms involved that result in selective advantage to some community members. Positive, negative or neutral interactions can occur between a very wide range of soil bacteria and fungi. These effects include both stimulation and inhibition of growth, by 40 and 60%, respectively, and enzyme production. These effects are usually transient, e.g. removal of an antagonist is followed by complete recovery. Up- and down-regulation of gene expression, by mRNA and protein profiling has been demonstrated. VOCs have played an important role during the evolution of microorganisms in the context of their communities. This revised version was published online in August 2006 with corrections to the Cover Date.     

A structurally conserved water molecule in Rossmann dinucleotide-binding domains

A computational comparison of 102 high-resolution (相似文献   

Plasticity in structure and interactions is critical for the action of indolicidin,an antibacterial peptide of innate immune origin

The comparative analysis of two cationic antibacterial peptides of the cathelicidin family-indolicidin and tritrypticin-enabled addressing the structural features critical for the mechanism of indolicidin activity. Functional behavior of retro-indolicidin was found to be identical to that of native indolicidin. It is apparent that the gross conformational propensities associated with retro-peptides resemble those of the native sequences, suggesting that native and retro-peptides can have similar structures. Both the native and the retro-indolicidin show identical affinities while binding to endotoxin, the initial event associated with the antibacterial activity of cationic peptide antibiotics. The indolicidin-endotoxin binding was modeled by docking the indolicidin molecule in the endotoxin structure. The conformational flexibility associated with the indolicidin residues, as well as that of the fatty acid chains of endotoxin combined with the relatively strong structural interactions, such as ionic and hydrophobic, provide the basis for the endotoxin-peptide recognition. Thus, the key feature of the recognition between the cationic antibacterial peptides and endotoxin is the plasticity of molecular interactions, which may have been designed for the purpose of maintaining activity against a broad range of organisms, a hallmark of primitive host defense.     

The role of aromatic residues in the hydrophobic core of the villin headpiece subdomain

Small autonomously folding proteins are of interest as model systems to study protein folding, as the same molecule can be used for both experimental and computational approaches. The question remains as to how well these minimized peptide model systems represent larger native proteins. For example, is the core of a minimized protein tolerant to mutation like larger proteins are? Also, do minimized proteins use special strategies for specifying and stabilizing their folded structure? Here we examine these questions in the 35‐residue autonomously folding villin headpiece subdomain (VHP subdomain). Specifically, we focus on a cluster of three conserved phenylalanine (F) residues F47, F51, and F58, that form most of the hydrophobic core. These three residues are oriented such that they may provide stabilizing aromatic–aromatic interactions that could be critical for specifying the fold. Circular dichroism and 1D‐NMR spectroscopy show that point mutations that individually replace any of these three residues with leucine were destabilized, but retained the native VHP subdomain fold. In pair‐wise replacements, the double mutant that retains F58 can adopt the native fold, while the two double mutants that lack F58 cannot. The folding of the double mutant that retains F58 demonstrates that aromatic–aromatic interactions within the aromatic cluster are not essential for specifying the VHP subdomain fold. The ability of the VHP subdomain to tolerate mutations within its hydrophobic core indicates that the information specifying the three dimensional structure is distributed throughout the sequence, as observed in larger proteins. Thus, the VHP subdomain is a legitimate model for larger, native proteins.     

Mapping and characterization of the functional epitopes of tissue inhibitor of metalloproteinases (TIMP)-3 using TIMP-1 as the scaffold: a new frontier in TIMP engineering

Tumor necrosis factor-alpha (TNF-alpha) converting enzyme (TACE/ADAM-17) is responsible for the release of TNF-alpha, a potent proinflammatory cytokine associated with many chronic debilitating diseases such as rheumatoid arthritis. Among the four variants of mammalian tissue inhibitor of metalloproteinases (TIMP-1 to -4), TACE is specifically inhibited by TIMP-3. We set out to delineate the basis for this specificity by examining the solvent accessibility of every epitope on the surface of a model of the truncated N-terminal domain form of TIMP-3 (N-TIMP-3) in a hypothetical complex with the crystal structure of TACE. The epitopes suspected of interacting with TACE were systematically transplanted onto N-TIMP-1. We succeeded in transforming N-TIMP-1 into an active inhibitor for TACE (K(i)(app) 15 nM) with the incorporation of Ser4, Leu67, Arg84, and the TIMP-3 AB-loop. The combined effects of these epitopes are additive. Unexpectedly, introduction of "super-N-TIMP-3" epitopes, defined in our previous work, only impaired the affinity of N-TIMP-1 for TACE. Our mutagenesis results indicate that TIMP-3-TACE interaction is a delicate process that requires highly refined surface topography and flexibility from both parties. Most importantly, our findings confirm that the individual characteristics of TIMP could be transplanted from one variant to another.     

Crystal structure of a major secreted protein of Mycobacterium tuberculosis-MPT63 at 1.5-A resolution

MPT63 is a small, major secreted protein of unknown function from Mycobacterium tuberculosis that has been shown to have immunogenic properties and has been implicated in virulence. A BLAST search identified that MPT63 has homologs only in other mycobacteria, and is therefore mycobacteria specific. As MPT63 is a secreted protein, mycobacteria specific, and implicated in virulence, MPT63 is an attractive drug target against the deadliest infectious disease, tuberculosis (TB). As part of the TB Structural Genomics Consortium, the X-ray crystal structure of MPT63 was determined to 1.5-Angstrom resolution with the hope of yielding functional information about MPT63. The structure of MPT63 is an antiparallel beta-sandwich immunoglobulin-like fold, with the unusual feature of the first beta-strand of the protein forming a parallel addition to the small antiparallel beta-sheet. MPT63 has weak structural similarity to many proteins with immunoglobulin folds, in particular, Homo sapiens beta2-adaptin, bovine arrestin, and Yersinia pseudotuberculosis invasin. Although the structure of MPT63 gives no conclusive evidence to its function, structural similarity suggests that MPT63 could be involved in cell-host interactions to facilitate endocytosis/phagocytosis.     

Infection of macaques with a molecular clone,SHIVSF33A2, provides evidence for tissue specific variants

Infection of rhesus macaques with chimeric simian-human immunodeficiency viruses (SHIV) is an established model to study acquired immunodeficiency syndrome (AIDS) pathogenesis. Such a controlled system allows for detailed analysis of the molecular determinants of viral pathogenesis in addition to studying host-specific immune responses that modulate disease progression. Furthermore, the use of a pathogenic molecular clone affords the opportunity to study both viral evolution within a host and to examine the generation of tissue specific variants. In this report we describe viral diversification within tissues of two rhesus macaques infected intravenously with the CXCR4-specific molecular clone SHIVSF33A2. Heteroduplex tracking analysis (HTA) was used to determine the complexity of viral DNA within distinct lymphoid tissues. Not surprising, heterogeneity of the proviral quasispecies in tissues obtained during the acute infection was limited. However, tissues obtained at necropsy harbored a more diverse and often different population of env variants. As the inoculating virus is a molecular clone, the variants generated are likely due to the presence of tissue specific selective forces rather than a founder's effect.     

Spontaneous pancreatic islet amyloidosis in 40 baboons

Spontaneous amyloidosis occurs in many nonhuman primate species but remains difficult to diagnose and treat. Nonhuman primates continue to offer promise as animal models in which to study amyloidosis in humans. Amyloidosis was not diagnosed clinically but was found histologically in four male and 36 female baboons. The baboons averaged 18 years of age at death (range, 7-28 years). Clinical signs, if present, were hyperglycemia and cachexia. Blood glucose values were elevated in 12 of 30 baboons with available clinical pathology data. Four baboons had been clinically diagnosed as diabetic and three were treated with insulin. Amyloid was found in the islets of Langerhans of the pancreas in 40 baboons; 35 baboons had amyloid only in the islets of Langerhans. Amyloid was found in nonislet tissue of baboons as follows: five, nonislet pancreas; four, intestine and adrenal; three, kidney; two, prostate and spleen; and one each, lymph node, liver, gall bladder, stomach, tongue, urinary bladder, and salivary gland. Sections of paraffin-embedded tissues were evaluated for amyloid with hematoxylin and eosin (HE) and congo red (CR) staining, and using immunohistochemistry for human islet amyloid polypeptide (IAPP), calcitonin gene-related peptide (CGRP), glucagon, pancreatic polypeptide (PP), somatostatin (SS), and porcine insulin. Islet amyloid was positive with HE in 40 baboons, with CR in 39 baboons, and with IAPP and CGRP in 35 baboons. IAPP and CGRP only stained islet amyloid. PP, SS, glucagon, and porcine insulin did not stain amyloid. Islet amyloidosis in the baboon appears to be difficult to diagnose clinically, age-related, and similar to islet amyloidosis in other species. The baboon may be a good model for the study of islet amyloidosis in humans.     

Water deficits and hydraulic limits to leaf water supply

Many aspects of plant water use -- particularly in response to soil drought -- may have as their basis the alteration of hydraulic conductance from soil to canopy. The regulation of plant water potential (Psi) by stomatal control and leaf area adjustment may be necessary to maximize water uptake on the one hand, while avoiding loss of hydraulic contact with the soil water on the other. Modelling the changes in hydraulic conductance with pressure gradients in the continuum allows the prediction of water use as a function of soil environment and plant architectural and xylem traits. Large differences in water use between species can be attributed in part to differences in their 'hydraulic equipment' that is presumably optimized for drawing water from a particular temporal and spatial niche in the soil environment. A number of studies have identified hydraulic limits as the cause of partial or complete foliar dieback in response to drought. The interactions between root:shoot ratio, rooting depth, xylem properties, and soil properties in influencing the limits to canopy water supply can be used to predict which combinations should optimize water use in a given circumstance. The hydraulic approach can improve our understanding of the coupling of canopy processes to soil environment, and the adaptive significance of stomatal behaviour.     

Pea aphid clonal resistance to the endophagous parasitoid Aphidius ervi

The physiological mechanism of resistance to the endophagous braconid Aphidius ervi Haliday (Hymenoptera, Braconidae) by a pink clone (PC) of Acyrthosiphon pisum (Harris) (Homoptera, Aphididae) has been investigated. Comparative data on parasitoid development and associated host biochemical changes in the resistant PC aphids and in a susceptible green clone (GC) of A. pisum are reported. When the PC aphids were attacked as early 4th instars, the developing parasitoid larvae showed a strongly reduced increase in size, compared to those synchronously developing in GC aphids, and were unable to produce a regular mummy. In contrast, parasitism of 2nd instar PC aphids, allowed completion of parasitoid development, but adults had a prolonged developmental time, due to a longer duration of parasitoid’s final (3rd) instar. In all cases, teratocytes, cells deriving from the A. ervi serosal membrane, and the proteins abundantly synthesised by them, were never found in the haemolymph of parasitised PC aphids. Host castration, as demonstrated by total protein incorporation into reproductive tissues, was total in the majority of early (2nd instar) parasitised host aphids, while it was limited when later instars (4th) of PC aphids were parasitised. This is partly due to the absence of the cytolytic activity of teratocytes on host embryos, which, through their persistence, may compete for nutritional resources with the developing parasitoid larvae. In parasitised PC aphids, this competitive effect is further aggravated for the parasitoid by the absence of the regulated amino acid titre increase in the host haemolymph, which is regularly observed in GC aphids. Failure of teratocyte development in the PC clone of the pea aphid is, then, the major functional constraint accounting for the reduction/inhibition of A. ervi larval growth. The reported results allow to assess in vivo the role of teratocytes in the host physiological redirection and nutritional exploitation by the parasitoid, and to integrate and validate the proposed physiological model of host-parasitoid interactions in the system A. pisum-A.ervi.