Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita

Plant-parasitic nematodes are major agricultural pests worldwide and novel approaches to control them are sorely needed. We report the draft genome sequence of the root-knot nematode Meloidogyne incognita, a biotrophic parasite of many crops, including tomato, cotton and coffee. Most of the assembled sequence of this asexually reproducing nematode, totaling 86 Mb, exists in pairs of homologous but divergent segments. This suggests that ancient allelic regions in M. incognita are evolving toward effective haploidy, permitting new mechanisms of adaptation. The number and diversity of plant cell wall-degrading enzymes in M. incognita is unprecedented in any animal for which a genome sequence is available, and may derive from multiple horizontal gene transfers from bacterial sources. Our results provide insights into the adaptations required by metazoans to successfully parasitize immunocompetent plants, and open the way for discovering new antiparasitic strategies.     

A de novo designed N-terminal disulphide bridge stabilizes the Trichoderma reesei endo-1,4-beta-xylanase II

We have successfully engineered a disulphide bridge into the N-terminal region of Trichoderma reesei endo-1,4-beta-xylanase II (XYNII) by substituting Thr-2 and Thr-28 with cysteine. The T2C:T28C mutational changes increased the half-life in thermal inactivation of this mesophilic enzyme from approximately 40 s to approximately 20 min at 65 degrees C, and from less than 10 s to approximately 6 min at 70 degrees C. Therefore, the N-terminal disulphide bridge enables the use of XYNII at substantially higher temperatures than permitted by its native mesophilic counterpart. Altogether, thermostability increased by about 15 degrees C. The kinetic properties of the mutant XYNII were maintained at the level of the wild type enzyme. Our findings demonstrated that a properly designed disulphide bridge, here within the N-terminal region of XYNII, can be very effective in resisting thermal inactivation.     

Cloning of an endo-1,4-beta-xylanase gene from Penicillium canescens and construction of multicopy strains

The complete gene xylA that encodes endo-1,4-beta-xylanase secreted by Penicillium canescens was cloned and sequenced. The coding region of the gene is separated by eight introns. The protein comprises 302 amino acids of the mature protein and 25 amino acids of the signal peptide. The xylanase of P. canescens belongs to the glycosyl hydrolase family 10. Nucleotide sequences for binding catabolite repression protein CREA and transactivator protein were detected in the promoter region. A set of multicopy strains displaying a seven-eightfold increase in xylanase yield was obtained. The fraction of xylanase in most productive strains amounted to 30-50% of the total secreted protein.     

Potato-associated bacteria and their antagonistic potential towards plant-pathogenic fungi and the plant-parasitic nematode Meloidogyne incognita (Kofoid & White) Chitwood

To study the effect of microenvironments on potato-associated bacteria, the abundance and diversity of bacteria isolated from the rhizosphere, phyllosphere, endorhiza, and endosphere of field grown potato was analyzed. Culturable bacteria were obtained after plating on R2A medium. The endophytic populations averaged 10(3) and 10(5) CFU/g (fresh wt.) for the endosphere and endorhiza. respectively, which were lower than those for the ectophytic microenvironments, with 10(5) and 10(7) CFU/g (fresh wt.) for the phyllosphere and rhizosphere, respectively. The composition and richness of bacterial species was microenvironment-dependent. The occurrence and diversity of potato-associated bacteria was additionally monitored by a cultivation-independent approach using terminal restriction fragment length polymorphism analysis of 16S rDNA. The patterns obtained revealed a high heterogeneity of community composition and suggested the existence of microenvironment-specific communities. In an approach to measure the antagonistic potential of potato-associated bacteria, a total of 440 bacteria was screened by dual testing for in vitro antagonism towards the soilborne pathogens Verticillium dahliae and Rhizoctonia solani. The proportion of isolates with antagonistic activity was highest for the rhizosphere (10%), followed by the endorhiza (9%), phyllosphere (6%), and endosphere (5%). All 33 fungal antagonists were characterized by testing their in vitro antagonistic mechanisms, including their glucanolytic, chitinolytic, pectinolytic, cellulolytic, and proteolytic activity, and by their BOX-PCR fingerprints. In addition, they were screened for their biocontrol activity against Meloidogyne incognita. Overall, nine isolates belonging to Pseudomonas and Streptomyces species were found to control both fungal pathogens and M. incognita and were therefore considered as promising biological control agents.     

The active site of an acidic endo-1,4-beta-xylanase of Aspergillus niger

The substrate binding site of an acidic endo-1,4-beta-xylanase (1,4-beta-D-xylan xylanohydrolase, EC 3.2.1.8) of Aspergillus niger was investigated using 1,4-beta-xylooligosaccharides (1-3H)-labelled at the reducing end. Bond cleavage frequencies and V/Km parameters of the oligosaccharides were determined under conditions of unimolecular hydrolysis and, according to the method of Suganuma et al. (J. Biochem. (Tokyo) (1978) 84, 293-316), used for evaluation of subsite affinities. The substrate binding site of the enzyme was found to consist of seven subsites, numbered -IV, -III, -II, -I, I, II and III, towards the subsite binding the reducing end unit of xyloheptaose. The catalytic groups were localized between subsites -I and I, the affinities of which have not been determined. All other subsites showed positive values of affinities for binding xylosyl residues. The values decrease from subsites -II and II, similarly in both directions. As a consequence of such an almost symmetric distribution of affinities around the catalytic groups, the enzyme cleaves preferentially the bonds in the oligosaccharides which are most distant from both terminals. Thus, the acidic A. niger beta-xylanase appears to be an endo-1,4-beta-xylanase attacking polymeric substrates in a random fashion. This conclusion was supported by viscosimetric measurements with carboxymethylxylan as a substrate.     

Synthesis and hydrolysis of 1,3-beta-xylosidic linkages by endo-1,4-beta-xylanase of Cryptococcus albidus

Purified extracellular endo-1,4-beta-xylanase (EC 3.2.1.8) of the yeast Cryptococcus albidus was found to catalyze not only the known 1,4-beta-transfer, but an alternative transglycosylation reaction leading to the formation of 1,3-beta-glycosidic linkages. From a mixture of products of beta-xylanase degradation of phenyl beta-D-xylopyranoside three xylooligosaccharide fractions, differing chromatographically from the 1,4-beta-linked products, were isolated by preparative paper chromatography. Their structure was elucidated by mass spectrometry, 13C-NMR spectroscopy and enzymic hydrolysis by beta-xylanase and beta-xylosidase. The isomeric xylotriose was identified as 3-O-beta-D-xylopyranosyl-4-O-beta-D-xylopyranosyl-D-xylose. The fraction of isomeric tetrasaccharides was found to be represented mainly by 4-O-beta-D-xylopyranosyl-3-O-beta-D-xylopyranosyl-4-O-beta-D-xylopyranosyl- D-xylose. The xylooligosaccharides containing one 1,3-beta-linkage were also produced on the enzyme treatment of 1,4-beta-xylotriose and 1,4-beta-xylan. When treated with the enzyme responsible for their synthesis, the isomeric xylooligosaccharides were hydrolyzed at the 1,3-beta-linkage, despite the fact the enzyme does not attack 1,3-beta-xylan. The results are interpreted in the relation to the characterized four-subsite substrate-binding site of the enzyme.     

RNA interference of dual oxidase in the plant nematode Meloidogyne incognita

RNA interference (RNAi) is a powerful tool for the analysis of gene function in model organisms such as the nematode Caenorhabditis elegans. Recent demonstrations of RNAi in plant parasitic nematodes provide a stimulus to explore the potential of using RNAi to investigate disruption of gene function in Meloidogyne incognita, one of the most important nematode pests of global agriculture. We have used RNAi to examine the importance of dual oxidases (peroxidase and NADPH oxidase), a class of enzyme associated with extracellular matrix cross-linking in C. elegans. RNAi uptake by M. incognita juveniles is highly efficient. In planta infection data show that a single 4-h preinfection treatment with double-stranded RNA derived from the peroxidase region of a dual oxidase gene has effects on gene expression that are phenotypically observable 35 days postinfection. This RNAi effect results in a reduction in egg numbers at 35 days of up to 70%. The in vitro feeding strategy provides a powerful tool for identifying functionally important genes, including those that are potential targets for the development of new agrochemicals or transgenic resistance strategies.     

Biological control of root-knot nematode,Meloidogyne incognita infesting tomato

Talc based formulations of two antagonistic fungi, Acremonium strictum W. Gams and Aspergillus terreus Thom were tested separately and together for their ability to suppress the development of root-knot disease of tomato caused by the root-knot nematode, Meloidogyne incognita Kofoid & White in two consecutive trials (2007–08). Tomato seedlings were each inoculated with M. incognita at 2 infective second stage juveniles /g of soil. M. incognita caused up to 48% reduction in plant growth parameters compared to un-inoculated control. Control efficacy achieved by combined soil application of both fungi, in terms of galls/root system and soil population/50 ml of soil, was 66 and 69% respectively at 60 days of inoculation compared to control. Soil application by individual fungus did not achieve as much effectiveness as the biocontrol agents applied together. The combined treatment was found to have antagonistic effect on M. incognita development and increased plant vigor. Incorporation of fine powder of chickpea pod waste with talc powder was beneficial in providing additional nutrients to both plant and biocontrol agents and increased the activity of the nematophagous fungi in soil. A. strictum and A. terreus were successfully established in the rhizosphere of tomato plants up to the termination of the experiment.     

Three-dimensional structure of endo-1,4-beta-xylanase II from Trichoderma reesei: two conformational states in the active site.

The three-dimensional structure of endo-1,4-beta-xylanase II (XYNII) from Trichoderma reesei has been determined by X-ray diffraction techniques and refined to a conventional R-factor of 18.3% at 1.8 A resolution. The 190 amino acid length protein was found to exist as a single domain where the main chain folds to form two mostly antiparallel beta-sheets, which are packed against each other in parallel. The beta-sheet structure is twisted, forming a large cleft on one side of the molecule. The structure of XYNII resembles that of Bacillus 1,3-1,4-beta-glucanase. The cleft is an obvious suggestion for an active site, which has putative binding sites for at least four xylose residues. The catalytic residues are apparently the two glutamic acid residues (Glu86 and Glu177) in the middle of the cleft. One structure was determined at pH 5.0, corresponding to the pH optimum of XYNII. The second structure was determined at pH 6.5, where enzyme activity is reduced considerably. A clear structural change was observed, especially in the position of the side chain of Glu177. The observed conformational change is probably important for the mechanism of catalysis in XYNII.     

In vitro proteolysis of nematode FMRFamide-like peptides (FLPs) by preparations from a free-living nematode (Panagrellus redivivus) and two plant-parasitic nematodes (Heterodera glycines and Meloidogyne incognita)

Proteolytic activities in extracts from three nematodes, the plant parasites Heterodera glycines and Meloidogyne incognita, and the free-living Panagrellus redivivus, were surveyed for substrate preferences using a battery of seven FRET-modified peptide substrates, all derived from members of the large FMRF-amide like peptide (FLP) family in nematodes. Overall protease activity in P. redivivus was four- to fivefold greater than in either of the parasites, a result that might reflect developmental differences. Digestion of the M. incognita FLP KHEFVRFa (substrate Abz-KHEFVRF-Y(3-NO2)a) by M. incognita extract was sevenfold greater than with H. glycines extract and twofold greater than P. redivivus, suggesting species-specific preferences. Additional species differences were revealed upon screening 12 different protease inhibitors. Two substrates were used in the screen, Abz-KHEFVRF-Y(3-NO2)a and Abz-KPSFVRF-Y(3-NO2)a), which was digested equally by all three species. The effects of various inhibitor, substrate and extract source combinations on substrate digestion suggest that M. incognita differs significantly from P. redivivus and H. glycines in its complement of cysteine proteases, particularly cathepsin L-type protease.     

Interactions between the root-knot nematode Meloidogyne incognita and Glomus mosseae in banana

The effects of the interaction between the arbuscular mycorrhizal fungus Glomus mosseae and the root-knot nematode Meloidogyne incognita on growth and nutrition of micropropagated ;Grand Naine banana (Musa AAA) cultivar was studied under greenhouse conditions. Inoculation with two G. mosseae isolates significantly increased growth of plants in relation to non-mycorrhizal plants. Response to mycorrhizae was as effective as with an optimum P fertilization in promoting plant development for most growth parameters. Meloidogyne incognita had no apparent effect on the percentage of root colonization in mycorrhizal plants. In contrast, G. mosseae suppressed root galling and nematode buildup in the roots. The percentage of mycorrhizal colonization was high (over 80%) in low P fertilized plants, but optimum P rates for bananas (four times higher than low P) significantly reduced mycorrhizal colonization. Most elements were within sufficiency levels for banana with exception of N which was low for all treatments. Mycorrhizal plants fertilized with a low P rate showed higher N, P, K, Ca, and Mg contents as compared to non-mycorrhizal plants low in P with or without the nematode. Inoculation with G. mosseae favours growth of banana plants by enhancing plant nutrition and by suppressing nematode reproduction and galling during the early stages of plant development.     

Response of five lettuce cultivars to root-knot nematode, Meloidogyne incognita

The root-knot nematode, Meloidogyne incognito (Kofoid et White) Chitwood is an important pathogen of vegetables. Five commercial cultivars of lettuce (Lactuca sativa L.) were evaluated under greenhouse conditions for resistance to Meloidogyne incognita, Benguet population. Plants were inoculated with 1000 eggs collected from 'Apollo' tomato (Lycopersicon esculentum) roots. The degree of galling and number of egg masses were assessed 4 and 8 weeks after inoculation. Host plant response was classified as immune, highly resistant, resistant, moderately resistant, intermediate, moderately susceptible, and highly susceptible based on the resistance index of Kouamè et at., 1998 [RI = (gall2 + egg2)]. Inoculation of 1000 eggs/plant significantly affected the growth and yield of the five lettuce cultivars 4 and 8 weeks after inoculation. A significant interaction was observed between treatment and cultivar during the two evaluation periods in terms of marketable and non-marketable yield, plant height, root weight, number of galls and number of egg masses. A reduction in growth and yield was observed in the cultivars Ballon, Lollo Rosa and Red Wave. Significant differences were noted in the number of galls and egg masses among the different cultivars tested. The highest average number of galls was obtained from the cultivars Red Wave, Ballon and Lollo Rosa. Cultivar Ballon had the highest average number of recovered nematode while Gilaben had the lowest with 15 and 4 per roots, respectively after 4 weeks inoculation. After 8 weeks, nematode was highest in cultivar Red Wave (615) and lowest in Great Lakes (70). Based on the host response, cultivars Great Lakes and Gilaben were rated highly resistant and resistant, respectively, while Red Wave, Ballon and Lollo Rosa were rated intermediate.     

Differential gene expression in Arabidopsis following infection by plant-parasitic nematodes Meloidogyne incognita and Heterodera schachtii

Whole genome microarrays were used to study plant gene expression in mature Meloidogyne incognita -induced galls in Arabidopsis. We found 959 genes to be significantly differentially expressed, and two-thirds of these were down-regulated. Microarray results were confirmed by qRT-PCR. The temporal and spatial responses of four differentially expressed genes were analysed using GUS reporter plants following infection with M. incognita and the cyst nematode Heterodera schachtii . The ammonium transporter gene AtAMT1;2 was consistently and locally repressed in response to both nematodes at all developmental stages. The lateral organ boundary domain gene LBD41 showed up-regulation in the feeding sites of both nematode species, although there was variation in expression in saccate H. schachtii female feeding sites. Expression of an actin depolymerizing factor ADF3 and a lipid transfer protein was induced in feeding sites of both nematodes at the fusiform stage and this persisted in feeding sites of saccate M. incognita . These results contribute to the knowledge of how plant gene expression responds to parasitism by these nematodes as well as highlighting further differences in the mechanisms of development and maintenance of these feeding site structures.     

Biocontrol of root-knot nematode Meloidogyne incognita by the isolates of Bacillus on tomato

Fifteen isolates of Bacillus, isolated from the root-knot nematode suppressive soils, were used for the biocontrol of Meloidogyne incognita on tomato. Bacillus isolates B1, B4, B5 and B11 caused greater inhibitory effect on hatching of M. incognita than caused by other isolates. In addition, these isolates (B1, B4, B5 and B11) caused greater colonisation of tomato roots and also caused greater increase in the growth of tomato seedling than caused by other isolates. All the isolates of Bacillus were able to increase growth of tomato and caused reduction in galling and nematode multiplication in green house tests. Isolates B1, B4, B5 and B11 caused a greater increase in growth of tomato and higher reduction in galling and nematode multiplication than other isolates in a green house test. These isolates were also tested for hydrogen cyanide (HCN) and indole acetic acid productions. Only one isolate (B13) produced HCN out of 15 tested. On the other hand, isolates B5, B11, B4 and B1 showed greater production of IAA than the other 11 isolates tested. This study suggests that Bacillus isolates B5, B11, B4 and B1 may be used for the biocontrol of M. incognita on tomato.