De novo assembly, gene annotation, and marker discovery in stored-product pest Liposcelis entomophila (Enderlein) using transcriptome sequences

Background

As a major stored-product pest insect, Liposcelis entomophila has developed high levels of resistance to various insecticides in grain storage systems. However, the molecular mechanisms underlying resistance and environmental stress have not been characterized. To date, there is a lack of genomic information for this species. Therefore, studies aimed at profiling the L. entomophila transcriptome would provide a better understanding of the biological functions at the molecular levels.

Methodology/Principal Findings

We applied Illumina sequencing technology to sequence the transcriptome of L. entomophila. A total of 54,406,328 clean reads were obtained and that de novo assembled into 54,220 unigenes, with an average length of 571 bp. Through a similarity search, 33,404 (61.61%) unigenes were matched to known proteins in the NCBI non-redundant (Nr) protein database. These unigenes were further functionally annotated with gene ontology (GO), cluster of orthologous groups of proteins (COG), and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. A large number of genes potentially involved in insecticide resistance were manually curated, including 68 putative cytochrome P450 genes, 37 putative glutathione S-transferase (GST) genes, 19 putative carboxyl/cholinesterase (CCE) genes, and other 126 transcripts to contain target site sequences or encoding detoxification genes representing eight types of resistance enzymes. Furthermore, to gain insight into the molecular basis of the L. entomophila toward thermal stresses, 25 heat shock protein (Hsp) genes were identified. In addition, 1,100 SSRs and 57,757 SNPs were detected and 231 pairs of SSR primes were designed for investigating the genetic diversity in future.

Conclusions/Significance

We developed a comprehensive transcriptomic database for L. entomophila. These sequences and putative molecular markers would further promote our understanding of the molecular mechanisms underlying insecticide resistance or environmental stress, and will facilitate studies on population genetics for psocids, as well as providing useful information for functional genomic research in the future.

Cholinesterase activity in Gammarus pulex (Crustacea Amphipoda): Characterization and effects of chlorpyrifos

The aim of this study was to characterize cholinesterase (ChE) activity in Gammarus pulex, an abundant and ecologically relevant species of the European stream environment. Biochemical and pharmacological properties were tested using different substrates (acetylthiocholine iodide, propionylthiocholine iodide and butyrylthiocholine iodide) and selective inhibitors (eserine sulfate, BW284c51 and iso-OMPA). In a second part, the in vitro and in vivo effects of a widely used organophosphorous pesticide, chlorpyrifos, on ChE activity were investigated. The results suggest that G. pulex possess only one ChE which displays the typical properties of an acetylcholinesterase, since: (1) it hydrolyses to the substrate acetylthiocholine at a higher rate than all other tested substrates and (2) it is highly sensitive to eserine sulphate and BW284c51, but not to iso-OMPA. In vitro and in vivo inhibitions were observed for highly different contamination levels, which suggests that bioaccumulation and biotransformation mechanisms are involved. In vivo AChE inhibition was observed at realistic environmental concentrations, with lethal effects appearing at inhibitions higher than 50%. The results of this study show the value of G. pulex as a sentinel organism for environmental assessment.

New friendly tools for users of ESTHER, the database of the α/β-hydrolase fold superfamily of proteins

The structural alpha/beta-hydrolase fold is characterized by a beta-sheet core of five to eight strands connected by alpha-helices to form a alpha/beta/alpha sandwich. The superfamily members, exemplified by the cholinesterases, diverged from a common ancestor into a number of hydrolytic enzymes displaying a wide range of substrate specificities, along with proteins with no recognized hydrolytic activity. In the enzymes, the catalytic triad residues are presented on loops of which one, the nucleophile elbow, is the most conserved feature of the fold. Of the other proteins, which all lack from one to all of the catalytic residues, some may simply be 'inactive' enzymes while others have been shown to be involved in heterologous surface recognition functions. The ESTHER (for esterases, alpha/beta-hydrolase enzymes and relatives) database (http://bioweb.ensam.inra.fr.esther) gathers and annotates all the published pieces of information (gene and protein sequences; biochemical, pharmacological, and structural data) related to the superfamily, and connects them together to provide the bases for studying structure-function relationships within the superfamily. The most recent developments of the database are presented.

The origin of the molecular diversity and functional anchoring of cholinesterases

Vertebrates possess two cholinesterases, acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) which both hydrolyze acetylcholine, but differ in their specificity towards other substrates, and in their sensitivity to inhibitors. In mammals, the AChE gene produces three types of coding regions through the choice of 3' splice acceptor sites, generating proteins which possess the same catalytic domain, associated with distinct C-terminal peptides. AChE subunits of type R ('readthrough') produce soluble monomers; they are expressed during development and induced by stress in the mouse brain. AChE subunits of type H ('hydrophobic') produce GPI-anchored dimers, but also secreted molecules; they are mostly expressed in blood cells. Subunits of type T ('tailed') exist for both AChE and BChE. They represent the enzyme forms expressed in brain and muscle. These subunits generate a variety of quaternary structures, including homomeric oligomers (monomers, dimers, tetramers), as well as hetero-oligomeric assemblies with anchoring proteins, ColQ and PRiMA. Mutations in the four-helix bundle (FHB) zone of the catalytic domain indicate that subunits of type H and T use the same interaction for dimerization. On the other hand, the C-terminal T peptide is necessary for tetramerization. Four T peptides, organized as amphiphilic alpha helices, can assemble around proline-rich motifs of ColQ or PRiMA. The association of AChE(T) or BChE subunits with ColQ produces collagen-tailed molecules, which are inserted in the extracellular matrix, e.g. in the basal lamina of neuromuscular junctions. Their association with PRiMA produces membrane-bound tetramers which constitute the predominant form of cholinesterases in the mammalian brain; in muscles, the level of PRiMA-anchored tetramers is regulated by exercise, but their functional significance remains unknown. In brain and muscles, the hydrolysis of acetylcholine by cholinesterases, in different contexts, and their possible noncatalytic functions clearly depend on their localization by ColQ or PRiMA.

Distribution profiles of paraoxonase and cholinesterase phenotypes in a Spanish population

The paraoxonase/arylesterase phenotype was measured in a Spanish population as previous studies have reported that the polymorphic variation in serum paraoxonase activity may affect the metabolism of organophosphates in individuals at risk of chronic intoxication. The prevalence of congenital deficiency in serum cholinesterase was also established in order to ascertain whether individuals with a congenital defect would be at a higher risk against a potential organophosphate exposure. We consider it useful to incorporate these two biomarkers into the health programme of agricultural workers with the purpose of monitoring workers who spray organophosphate pesticides, as they provide reliable indications of early-stage effects related to biochemical alterations that might precede overt clinical pictures.

[Cholinesterase]

Since the chromatographic separation of cholinesterase (ChE) by Malström in 1956 many investigator studied ChE isozyme, Harris divided five spots by two dimensional paper electrophoresis and starchgel electrophoresis, and referred as C1 C2 C3 C4. Clinically, Juul separated ChE 12 bands by polyacrylamidegel electrophoresis. We separated ChE as five bands using polyacrylamidegel electrophoresis, revealing fusion and deformity of the band. Takahashi et al reported separation of band using acetyl and butyrylthiocholine as substrate. They found abnormal band in liver cirrhosis, however they have thought it acetyl cholinesterase. Hada et al revealed a defect of band II in liver cirrhosis. They investigated ChE isozyme using affinity electrophoresis with Concanavalin A (Con A) and wheat germ agglutinin (WGA). They found disappearance of band 2, Con A and WGA containing agarose gel electrophoresis seem to be useful method in differentiating liver cirrhosis from chronic hepatitis. The number of isozyme fraction exhibited a species related variations in laboratory animals. Rats, hamsters guinea pigs, rabbits, dogs, monkeys, pigs, horses and quails have 4, 3, 4, 3-5, 3, 3, 4 and 3 isozyme bands, respectively.

Nature of cholinesterase in the rat retina

The occurrence of cholinesterases has been demonstrated in retinas of several mammalian species. Histochemical staining techniques indicate that the acetylcholinesterases (AChE) are present in amacrine cells and their neighboring bipolar cells. However, the nature of retinal cholinesterases and their interactions with specific cholinesterase inhibitors are not known. Therefore, we have studied the inhibition of the rat retinal cholinesterase activity by BW284C51, a selective inhibitor of AChE, and iso-OMPA, a selective inhibitor of butyrylcholinesterase (BChE). Retinas from Zivic-Miller rats were solubilized by sonication in phosphate buffer (0.134 M, pH 7.2) at 4 degrees C for 20 min. The cholinesterase activity in the sonicate was determined by a radiometric method using 14C-acetylcholine (ACh) as substrate (10(-2) M). Excess 14C-ACh was adsorbed by Amberlite CG-120 cation exchange resin. 14C-acetate formed and retained in the aqueous medium was determined by liquid scintillation counting. This study gave the following results: (a) Rat retinal sonicate gave total cholinesterase activity of 3.76 mumol of ACh hydrolyzed/mg protein/15 min; (b) This activity was inhibited by BW284C51 (IC50, 0.115 microM). Iso-OMPA (IC50, 500 microM) did not cause significant inhibition at 0.115 microM. These observations suggest that the rat retinal cholinesterase is predominantly AChE.

Interspecific variations of cerebral endothelial cholinesterases in rodents and carnivores

The cholinesterase equipment of cerebral microvessels was studied in some rodents and carnivores using the Koelle-Friedenwald histochemical method with 3 artificial substrates and specific inhibitors for butyrylcholinesterase or acetylcholinesterase. Our observations reveal a great heterogeneity in cholinesterase types and their distribution in each of the different species studied. Only in the rat, butyrylcholinesterase appears to be a marker for the microvessels provided with a blood-brain barrier.

Amphiphilic and nonamphiphilic forms of Torpedo cholinesterases: I. Solubility and aggregation properties

We report an analysis of the solubility and hydrophobic properties of the globular forms of acetylcholinesterase (AChE) and butyrylcholinesterase (BuChE) from various Torpedo tissues. We distinguish globular nonamphiphilic forms (Gna) from globular amphiphilic forms (Ga). The Ga forms bind micelles of detergent, as indicated by the following properties. They are converted by mild proteolysis into nonamphiphilic derivatives. Their Stokes radius in the presence of Triton X-100 is approximately 2 nm greater than that of their lytic derivatives. The G2a forms fall in two classes. Class I contains molecules that aggregate in the absence of detergent, when mixed with an AChE-depleted Triton X-100 extract from electric organ. AChE G2a forms from electric organs, nerves, skeletal muscle, and erythrocyte membranes correspond to this type, which is also detectable in detergent-soluble (DS) extracts of electric lobes and spinal cord. Class II forms never aggregate but only present a slight shift in sedimentation coefficient, in the presence or absence of detergent. This class contains the AChE G2a forms of plasma and of the low-salt-soluble (LSS) fractions from spinal cord and electric lobes. The heart possesses a BuChE G2a form of class II in LSS extracts, as well as a similar G1a form. G4a forms of AChE, which are solubilized only in the presence of detergent and aggregate in the absence of detergent, represent a large proportion of cholinesterase in DS extracts of nerves and spinal cord, together with a smaller component of G4a BuChE. These forms may be converted to nonamphiphilic derivatives by Pronase. Nonaggregating G4a forms exist at low levels in the plasma (BuChE) and in LSS extracts of nerves (BuChE) and spinal cord (AChE).

Amphiphilic and nonamphiphilic forms of Torpedo cholinesterases: II. Electrophoretic variants and phosphatidylinositol phospholipase C-sensitive and -insensitive forms

We report an electrophoretic analysis of the hydrophobic properties of the globular forms of acetylcholinesterase (AChE) and butyrylcholinesterase (BuChE) from various Torpedo tissues. In charge-shift electrophoresis, the rate of electrophoretic migration of globular amphiphilic forms (Ga) is increased at least twofold when the anionic detergent deoxycholate is added to Triton X-100, whereas that of globular nonamphiphilic forms (Gna) is not modified. The G2a forms of the first class, as defined by their aggregation properties, are converted to nonamphiphilic derivatives by phosphatidylinositol phospholipase C (PI-PLC) and human serum phospholipase D (PLD). AChE G2a forms from electric organs, nerves, skeletal muscle, and erythrocyte membranes correspond to this type, which also exists in very small quantities in detergent-solubilized extracts of electric lobes and spinal cord. They present different electrophoretic mobilities, so that each of these tissues contains a distinct "electromorph," or two in the case of electric organs. The G2a forms of the second class (AChE in plasma, BuChE in heart), as well as G4a forms of AChE and BuChE, are insensitive to PI-PLC and PLD but may be converted to nonamphiphilic derivatives by Pronase.

[Application to an automatic system of a direct method for determining atypical variants of cholinesterase using succinyldithiocholine as substrate]

The determination of human serum cholinesterase (EC 3.1.1.8) is frequently requested to detect patients with atypical forms of the enzyme which reacts abnormally with succinylcholine (suxamethonium), employed as a neuromuscular blocking agent. Usually, for biochemical identification of succinylcholine sensitive individuals the standard reaction is run with and without the inhibitors, notably dibucaine. A new test for direct determination of succinylcholine sensitive individuals which use a substrate analogue of succinylcholine was applied to a automated instrument. The linearity, precision, recovery, interference and correlation of the method have been evaluated. We have estimated the reference intervals for a population of 364 healthy subjects subdivided for sex, three atypical homozygotes and two atypical heterozygotes. On the basis of analytical performance we can conclude that this test may offer a further parameter for preoperative screening of individuals with an abnormal response to the muscle relaxant succinylcholine, thus avoiding the determination of genotype by measurement of dibucaine number.

Brain cholinesterases. Differentiation of target enzymes for toxic organophosphorus compounds

Cholinesterases in hen brain were characterized with respect to inhibition kinetics and substrate specificity. Three organophosphorus inhibitors were used: diethyl p-nitrophenyl phosphate (Paraoxon, E 600), di-isopropylphosphorofluoridate (DFP), and N,N'-di-isopropylphosphorodiamidic fluoride (Mipafox). The kinetics of irreversible cholinesterase inhibition were studied using two substrates, acetylthiocholine and butyrylthiocholine. The inhibition curves were analysed by the method of iterative elimination of exponential functions. Final classification of the different enzymes was done by combining two inhibitors in sequential inhibition expts. Six cholinesterases were shown to hydrolyse choline esters in hen brain, one was identified as acetylcholinesterase (EC 3.1.1.7) and one as cholinesterase (EC 3.1.1.8). Four enzymes can be classified as intermediate type cholinesterases according to their substrate specificity and to their inhibition constants. The possible role of different brain cholinesterases for the development of atypical symptoms following organophosphate intoxication is discussed.

On genetically determined human serum cholinesterases

The existence of genetically determined human serum cholinesterase variants (actlcholine acyl-hydrolase; EC 3.1.1.8) has been recognized by the use of a short acting muscle relaxant, suxamethonium. This polymorphism is now explained by at least four alleles belonging to an autosomal locus Ch1 or E1 depending on the nomenclature. These are: the usual gene, the dibucaine-resistant gene, the fluoride-resistant gene and the silent gene. At present, the modes of transmission for the silent genes is confusing and lack proper understanding. Another variant, not an allele of the first group, is recognized by gel electrophoresis, belong to a second locus Ch2 or E2. Evidence has been presented that many more rare serum cholinesterase variants may exist. Besides these genetic variants, normal serum cholinesterase is known to exist in multiple molecular forms. The present article attempts to discuss the polymorphism of human cholinesterase in relation to their chemical and genetic characteristics and their possible function.