A De Novo Transcriptomics Approach Reveals Genes Involved in Thrips Tabaci Resistance to Spinosad.

The onion thrip, Thrips tabaci (Thysanoptera: Thripidae) is a major polyphagous pest that attacks a wide range of economically important crops, especially Allium species. The thrip's damage can result in yield loss of up to 60% in onions (Allium cepa). In the past few decades, thrip resistance to insecticides with various modes of actions have been documented. These include resistance to spinosad, a major active compound used against thrips, which was reported from Israel. Little is known about the molecular mechanisms underlying spinosad resistance in T. tabaci. We attempted to characterize the mechanisms involved in resistance to spinosad using quantitative transcriptomics. Susceptible (LC50 = 0.6 ppm) and resistant (LC50 = 23,258 ppm) thrip populations were collected from Israel. An additional resistant population (LC50 = 117 ppm) was selected in the laboratory from the susceptible population. De novo transcriptome analysis on the resistant and susceptible population was conducted to identify differently expressed genes (DGEs) that might be involved in the resistance against spinosad. In this analysis, 25,552 unigenes were sequenced, assembled, and functionally annotated, and more than 1500 DGEs were identified. The expression levels of candidate genes, which included cytochrome P450 and vittelogenin, were validated using quantitative RT-PCR. The cytochrome P450 expression gradually increased with the increase of the resistance. Higher expression levels of vitellogenin in the resistant populations were correlated with higher fecundity, suggesting a positive effect of the resistance on resistant populations. This research provides a novel genetic resource for onion thrips and a comprehensive molecular examination of resistant populations to spinosad. Those resources are important for future studies concerning thrips and resistance in insect pests regarding agriculture.

Coping with High Temperature: A Unique Regulation in A. tumefaciens.

Elevation of temperature is a frequent and considerable stress for mesophilic bacteria. Therefore, several molecular mechanisms have evolved to cope with high temperature. We have been studying the response of Agrobacterium tumefaciens to temperature stress, focusing on two aspects: the heat-shock response and the temperature-dependent regulation of methionine biosynthesis. The results indicate that the molecular mechanisms involved in A. tumefaciens control of growth at high temperature are unique and we are still missing important information essential for understanding how these bacteria cope with temperature stress.

Persistent, circulative transmission of begomoviruses by whitefly vectors.

Begomoviruses comprise an emerging and economically important group of plant viruses exclusively transmitted by the sweetpotato whitefly Bemisia tabaci in many regions of the world. The past twenty years have witnessed significant progress in studying the molecular interactions between members of this virus group and B. tabaci. Mechanisms and proteins encoded by the insect vector and its bacterial symbionts, which have been shown to be important for virus transmission, have been identified and thoroughly studied. Despite the economic importance of this group of viruses and their impact on the global agriculture, progress in investigating the virus-vector interactions is moving slowly when compared with similar virus-vector systems in plants and animals. Major advances in this field and future perspectives will be discussed in this review.

Species-specific non-physical interference competition among mosquito larvae.

Individuals of different sex, size or developmental stage can compete differently and hence contribute distinctively to population dynamics. In species with complex life cycles such as insects, competitive ability is often positively correlated with larval developmental stage. Yet, little is known on how the development and survival of early-instars is influenced by interference from late-instar larvae, especially at low densities when exploitative competition is expected to be negligible. Furthermore, the specificity and mechanisms by which interference competition operates are largely unknown. We performed two complementary experiments aiming to quantify the competitive effects of late instar Ochlerotatus caspius on early instar larvae at low densities and under high resource supply rate. The first experiment examined the net effect of interference by 4(th) on 1(st) instar O. caspius larvae, relative to the effect of 1(st) instars on themselves. The second experiment examined the effect of species-specific, non-physical interference competition (i.e., cage larvae) by 4(th) on 1(st) instar O. caspius larvae at low or high densities. Specifically, we compared the responses of O. caspius larvae raised in the presence of caged con- or hetero-specific, Culiseta longiareolata, with that of larvae in the empty-cage control group. As expected, interference from late instar larvae had a net negative effect on the development rate of first instars. In contrast, the presence of caged con-specifics (non-physical interference) accelerated the development rate of O. caspius, however, this pattern was only evident at the low density. Notably, no such pattern was detected in the presence of caged hetero-specifics. These results strongly suggest the existence of species-specific growth regulating semiochemicals.

A photolyase-like protein from Agrobacterium tumefaciens with an iron-sulfur cluster.

Photolyases and cryptochromes are evolutionarily related flavoproteins with distinct functions. While photolyases can repair UV-induced DNA lesions in a light-dependent manner, cryptochromes regulate growth, development and the circadian clock in plants and animals. Here we report about two photolyase-related proteins, named PhrA and PhrB, found in the phytopathogen Agrobacterium tumefaciens. PhrA belongs to the class III cyclobutane pyrimidine dimer (CPD) photolyases, the sister class of plant cryptochromes, while PhrB belongs to a new class represented in at least 350 bacterial organisms. Both proteins contain flavin adenine dinucleotide (FAD) as a primary catalytic cofactor, which is photoreduceable by blue light. Spectral analysis of PhrA confirmed the presence of 5,10-methenyltetrahydrofolate (MTHF) as antenna cofactor. PhrB comprises also an additional chromophore, absorbing in the short wavelength region but its spectrum is distinct from known antenna cofactors in other photolyases. Homology modeling suggests that PhrB contains an Fe-S cluster as cofactor which was confirmed by elemental analysis and EPR spectroscopy. According to protein sequence alignments the classical tryptophan photoreduction pathway is present in PhrA but absent in PhrB. Although PhrB is clearly distinguished from other photolyases including PhrA it is, like PhrA, required for in vivo photoreactivation. Moreover, PhrA can repair UV-induced DNA lesions in vitro. Thus, A. tumefaciens contains two photolyase homologs of which PhrB represents the first member of the cryptochrome/photolyase family (CPF) that contains an iron-sulfur cluster.

The effect of steepness of temporal resource gradients on spatial root allocation.

Plants are able to discriminately allocate greater biomass to organs that grow under higher resource levels. Recent evidence demonstrates that split-root plants also discriminately allocate more resources to roots that grow under dynamically improving nutrient levels, even when their other roots grow in richer patches. Here, we further tested whether, besides their responsiveness to the direction of resource gradients, plants are also sensitive to the steepness of environmental trajectories. Split-root Pisum sativum plants were grown so that one of their roots developed under constantly-high nutrient levels and the other root was subjected to dynamically improving nutrient levels of variable steepness. As expected, plants usually allocated a greater proportion of their biomass to roots that developed under constantly high resource availability; however, when given a choice, they allocated greater biomass to roots that initially experienced relatively low but steeply improving nutrient availabilities than to roots that developed under continuously-high nutrient availability. Such discrimination was not observed when the roots in the poor patch experienced only gentler improvements in nutrient availability. The results are compatible with the notion that responsiveness to the direction and steepness of environmental gradients could assist annual plants to increase their performance by anticipating resource availabilities foreseeable before the end of their growing season. The results exemplify the ability of plants to integrate and utilize environmental information and execute adaptive behaviours which, until recently, were attributed only to animals with central nervous systems.

Proteomics of a plant pathogen: Agrobacterium tumefaciens.

Agrobacterium tumefaciens is an important plant pathogen which belongs to the α-proteobacteria. In addition, it has served as the main tool for plant molecular genetics. Here we focus on three major aspects: (i) proteomic mapping, (ii) the use of proteomics for the understanding of the response of A. tumefaciens to changes in environmental conditions and (iii) the analysis of the changes in genome expression following interaction with the host. These studies convey a global outlook on the functional genomics of A. tumefaciens and help to understand the physiology of this important organism.

Analysis of ultra acidic proteins by the use of anodic acidic gels.

Ultra acidic proteins, generated by posttranslational modifications, are becoming increasingly important due to recent evidence showing their function as regulatory elements or as intermediates in degradation pathways in bacteria. Such proteins are important in neurodegenerative diseases and embryonic development, and they include the Alzheimer-related tau (tau) protein (resulting from posttranslational modifications) and the phosphor-storage embryonic proteins. The ultra acidic proteins are difficult to study because standard two-dimensional gel electrophoresis is inadequate for their analysis. Here we describe a novel electrophoresis system of anodic acidic gels that can replace isoelectric focusing as the first dimension of separation in two-dimensional electrophoresis. The system is based on a sodium acetate buffer (pH 4.6), is compatible with traditional stains (e.g., Coomassie blue) as well as novel fluorescent dyes (e.g., Pro-Q Diamond), and is quantitative for the analysis of ultra acidic proteins. The anodic acidic gels were used for the functional classification of the ultra acidic part of the Bacillus subtilis proteome, showing significant improvement over traditional two-dimensional electrophoresis.

Light affects motility and infectivity of Agrobacterium tumefaciens.

Response to changes in light conditions involves a variety of receptors that can modulate gene expression, enzyme activity and/or motility. For the study of light-regulated effects of Agrobacterium tumefaciens, we used a global analysis approach - proteomics - and compared the protein patterns of dark- and light-grown bacteria. These analyses revealed a significant reduction of FlaA and FlaB - proteins of the flagellum - when the cells were grown in light. The light effect was confirmed by SDS-PAGE with isolated flagella. Quantitative PCR experiments showed a 10-fold increase of the transcription level of flaA, flaB and flaC within 20 min after the transfer from light to darkness. Electron microscopy revealed that these molecular events result in a light-induced reduction of the number of flagella per cell. These changes have major physiological consequences regarding motility, which is considerably reduced with exposure to light. The inhibitory effect of light on the motility is not unique to A. tumefaciens and was also seen in other species of the Rhizobiaceae. Previous studies suggested that the flagella function is significant for bacteria-plant interactions and bacterial virulence. In our studies, light reduced the attachment of A. tumefaciens to tomato roots and the virulence of the bacteria in a cucumber infection assay.

Mass spectrometry for monitoring micropollutants in water.

Surface water reservoirs and aquifers are exposed to contamination by thousands of micropollutants from industrial, pharmaceutical, agricultural and natural origins. Most developed and developing countries implement a water-quality regulation programme to prevent contamination by such chemicals at illegal concentrations. Traditionally, analytical methods based on gas chromatography-mass spectrometry or liquid chromatography with UV/fluorescence detection were used to monitor water quality. These methods require multistep sample preparation and several have low specificity. Nowadays, liquid chromatography tandem mass spectrometry has become a key technique for environmental analysis, allowing the detection of a wide range of polar and nonvolatile compounds. The use of this method has increased the specificity and confidence of identification, while reducing sample preparation to a minimum.

Protein conformational changes of Agrobacterium phytochrome Agp1 during chromophore assembly and photoconversion.

Phytochromes are widely distributed photochromic biliprotein photoreceptors. Typical bacterial phytochromes such as Agrobacterium Agp1 have a C-terminal histidine kinase module; the N-terminal chromophore module induces conformational changes in the protein that lead to modulation of kinase activity. We show by protein cross-linking that the C-terminal histidine kinase module of Agp1 mediates stable dimerization. The fragment Agp1-M15, which comprises the chromophore module but lacks the histidine kinase module, can also form dimers. In this fragment, dimer formation was stronger for the far-red-absorbing form Pfr than for the red-absorbing form Pr. The same or similar behavior was found for Agp1-M15Delta9N and Agp1-M15Delta18N, which lack 9 and 18 amino acids of the N-terminus, respectively. The fragment Agp1-M20, which is derived from Agp1-M15 by truncation of the C-terminal "PHY domain" (191 amino acids), can also form dimers, but dimerization is independent of irradiation conditions. The cross-linking data also showed that the PHY domain is in tight contact with Lys 16 of the protein and that the nine N-terminal amino acids mediate oligomer formation. Limited proteolysis shows that the hinge region between the chromophore module and the histidine kinase and a part of the PHY domain become exposed upon Pr to Pfr photoconversion.

GABA controls the level of quorum-sensing signal in Agrobacterium tumefaciens.

The concentration of GABA increases rapidly in wounded plant tissues, but the implication of this GABA pulse for plant-bacteria interactions is not known. Here we reveal that GABA stimulated the inactivation of the N-(3-oxooctanoyl)homoserine lactone (OC8-HSL) quorum-sensing signal (or "quormone") by the Agrobacterium lactonase AttM. GABA induced the expression of the attKLM operon, which was correlated to a decrease in OC8-HSL concentration in Agrobacterium tumefaciens cultures. The Agrobacterium GABA transporter Bra was required for this GABA-signaling pathway. Furthermore, transgenic tobacco plants with elevated GABA levels were less sensitive to A. tumefaciens C58 infection than were wild-type plants. These findings indicate that plant GABA may modulate quorum sensing in A. tumefaciens, thereby affecting its virulence on plants. Whereas GABA is an essential cell-to-cell signal in eukaryotes, here we provide evidence of GABA acting as a signal between eukaryotes and pathogenic bacteria. The GABA signal represents a potential target for the development of a strategy to control the virulence of bacterial pathogens.

OmpA of a septicemic Escherichia coli O78--secretion and convergent evolution.

OmpA is an important constituent of the outer membrane of Gram-negative bacteria. OmpA is involved in a variety of host-bacteria interactions, including crossing of the blood-brain barrier by E. coli strains causing newborn meningitis, and elicits a significant response by the immune system of the host. The bactericidal effect of neutrophil elastase (NE) is also attributed to degradation of the bacterial OmpA. Here we examined the OmpA of septicemic E. coli 078 strains and show that two surface-exposed loops are conserved among invasive strains of E. coli and other pathogenic Enterobacteriaceae. In addition, there is evidence for convergent evolution, implying the existence of selective pressure. Our results also indicate that large quantities of OmpA are secreted into the medium during all phases of growth, where it is present both in secreted vesicles and as a soluble secreted protein. We assume that secreted OmpA can play a role in protection of bacteria from NE by competitive inhibition. Support for this assumption was obtained from experiments indicating that addition of exogenous, purified OmpA reduces killing of bacteria by NE.

Probing the active site of homoserine trans-succinylase.

Homoserine trans-succinylase is the first enzyme in methionine biosynthesis of Escherichia coli and catalyzes the activation of homoserine via a succinylation reaction. The in vivo activity of this enzyme is subject to tight regulation by several mechanisms, including repression and activation of gene expression, feedback inhibition, temperature regulation and proteolysis. This complex regulation reflects the key role of this enzyme in bacterial metabolism. Here, we demonstrate--using proteomics and high-resolution mass spectrometry--that succinyl is covalently bound to one of the two adjacent lysine residues at positions 45 and 46. Replacing these lysine residues by alanine abolished the enzymatic activity. These findings position the lysine residues, one of which is conserved, at the active site.

Highly phosphorylated bacterial proteins.

We show in Gram-negative and Gram-positive bacteria the appearance of highly acidic proteins, which are highly phosphorylated. This group of proteins includes many cellular proteins, such as chaperones, biosynthetic, and metabolic enzymes. These proteins accumulate under stress conditions or under conditions, which overload the proteolytic system. Pulse chase experiments using radioactive phosphate indicate that the phosphorylated proteins have a short half-life, suggesting that they could be degradation intermediates. Moreover, results from in vitro experiments in Escherichia coli indicated that ribosomal proteins become susceptible to proteolysis after polyphosphorylation. Therefore, it is possible that the highly phosphorylated proteins represent a group of proteins tagged for degradation by phosphorylation. Such a tagging process may be involved in a general bacterial degradation pathway.

Two-dimensional reference map of Agrobacterium tumefaciens proteins.

Proteomics based on two-dimensional (2-D) gel electrophoresis of proteins followed by spot identification with mass spectrometry is a commonly used method for physiological studies. Physiological proteomics requires 2-D reference maps, on which most of the main proteins are identified. We present a reference map for the bacterial plant pathogen Agrobacterium tumefaciens proteins, which contains more than 300 entries with an isoelectric point (pI) between 4 and 7. The quantitative study of the proteins in the analytical window of the master gel demonstrated unique features, in comparison with other bacteria. In addition, a theoretical analysis of several protein parameters was performed and compared with the experimental results. A comparison of the theoretical molecular weight (MW) of the proteins and their theoretical pI with their vertical and horizontal migration distances, respectively, pointed out the existence of several proteins that strongly diverted from the graph trend-line. These proteins were clearly subjected to post-translational modifications, which changed their pI and/or MW. Additional support for post-translational modifications comes from the identification of multiple spots of the same gene products. Post-translational modifications appear to be more common than expected, at least for soluble proteins, as more than 10% of the proteins were associated with multiple spots.

Proteome analysis of plant-induced proteins of Agrobacterium tumefaciens.

Abstract A proteome study of Agrobacterium tumefaciens exposed to plant roots demonstrated the existence of a plant-dependent stimulon. This stimulon was induced by exposure to cut roots and consists of at least 30 soluble proteins (pI 4-7), including several proteins whose involvement in agrobacteria-host interactions has not been previously reported. Exposure of the bacteria to tomato roots also resulted in modification of the proteins: Ribosomal Protein L19, GroEL, AttM, and ChvE, indicating the significance of protein modifications in the interactions of agrobacteria with plants.

Protein aggregation in Escherichia coli: role of proteases.

Protein aggregation is involved in several human diseases, and presumed to be an important process in protein quality control. In bacteria, aggregation of proteins occurs during stress conditions, such as heat shock. We studied the protein aggregates of Escherichia coli during heat shock. Our results demonstrate that the concentration and diversity of proteins in the aggregates depend on the availability of proteases. Aggregates obtained from mutants in the Lon (La) protease contain three times more protein than wild-type aggregates and show the broadest protein diversity. The results support the assumption that protein aggregates are formed from partially unfolded proteins that were not refolded by chaperones or degraded by proteases.

Heat shock proteome of Agrobacterium tumefaciens: evidence for new control systems.

The regulation of Agrobacterium tumefaciens heat shock genes involves a transcriptional activator (RpoH) and repressor elements (HrcA-CIRCE). Using proteome analysis and mutants in these control elements, we show that the heat shock induction of 32 (out of 56) heat shock proteins is independent of RpoH and HrcA. These results indicate the existence of additional regulatory factors in the A. tumefaciens heat shock response.

Proteome analysis in the study of the bacterial heat-shock response.

In recent years, it has become clear that, in addition to the regulation of the expression of specific genes, there are global regulatory systems that control the simultaneous expression of a large number of genes in response to a variety of environmental stresses. The first of these global control systems, and of substantial importance, is the heat-shock response. The heat-shock response is characterized by the induction of a large set of proteins (heat-shock proteins-HSPs) upon shifts to higher temperature and upon exposure to conditions in which proteins are denatured (i.e., alcohols, heavy metals). The heat-shock response is universal and many of the heat-shock proteins are highly conserved among species. In bacteria, the heat-shock response has been studied extensively in several Gram-positive bacteria (Bacillus subtilis) and in the Gram-negative bacteria (i.e., Escherichia coli, Agrobacterium tumefaciens). The first recognition of the molecular abundance of the bacterial heat-shock proteins took place with the introduction of high-resolution two-dimensional polyacrylamide gels (2D gels) to analyze complex mixtures of cellular proteins. Two-dimensional gels, followed by mass spectrometry, were used to define the heat-shock stimulons in several bacteria, and to study the regulatory elements that control the heat-shock response. Here, we review the heat-shock response and its regulation in bacteria. The review will emphasize the use of proteome analysis in the study of this response, and will point out those open questions that can be investigated with proteomics, including mass spectrometry techniques.