Protein markers of Bursaphelenchus xylophilus Steiner & Buhrer, 1934 (Nickle, 1970) populations using quantitative proteomics and character compatibility

Abstract

The Pine Wood Nematode (PWN) Bursaphelenchus xylophilus is a severe forest pathogen in countries where it has been introduced and is considered a worldwide quarantine organism. In this study, protein markers for differentiating populations of this nematode were identified by studying differences among four selected Iberian and one American population. These populations were compared by quantitative proteomics (iTRAQ). From a total of 2860 proteins identified using the public database from the B. xylophilus genome project, 216 were unambiguous and significantly differentially regulated in the studied populations. Comparisons of their pairwise ratio were statistically treated and supported in order to convert them into discrete character states, suggesting that 141 proteins were not informative as population specific markers. Application of the Character Compatibility methodology on the remaining 75 proteins (belonging to families with different biological functions) excludes 27 which are incompatible among them. Considering only the compatible proteins, the method selects a subset of 30 specific unique protein markers which allowed the compared classification of the Iberian isolates. This approach makes it easier search for diagnostic tools and phylogenetic inference within species and populations of a pathogen exhibiting a high level of genetic diversity.

Phosphorylation coexists with O‐GlcNAcylation in a plant virus protein and influences viral infection

“…For the differential proteomics iTRAQ procedure, peptides resulting from Lys‐C/trypsin treatment were labelled using the iTRAQ 4‐plex kit (SCIEX), as described previously (Ciordia et al ., ), following this scheme: WT biological replica 1, tag‐114; SEC‐b2 biological replica 1, tag‐115; WT biological replica 2, tag‐116; SEC‐b2 biological replica 2, tag‐117. Labelled samples were pooled, dried and desalted using a SEP‐PAK C18 Cartridge (WATERS, Milford, MA, USA), and subjected to nanoLC‐ESI‐MS/MS TripleTOF after phosphopeptide enrichment (Methods S1).…”

Quantitative Proteomics Comparison of Total Expressed Proteomes of Anisakis simplex Sensu Stricto, A. pegreffii, and Their Hybrid Genotype

“…The biological independence of both experiments comparing four biological replicates of A. simplex and two other biological replicates for A. pegreffii and their common hybrids has been assesed by means of multifactorial correspondance analysis ( Figure 2 and Figure 3 ). Lastly, selected significant proteins ( Table 1 ) that acomplish the criteria for identification ( p < 0.05 FDR) were also submited to a direct test in order to convert the quantitative data of both experiments in qualitative one reflecting the expression protein tendence (up or down regulated) as binary data, as was formerly proposed [ 35 ].…”

“…Selection of the proteins which can be considered as taxonomic markers was done by coding the resulting quantification of proteins expression in the iTRAQ experiments to obtain significant discrete states (0, 1). Codification (0, 1) was based on level of signification of ratio (Log 2 ratios) of the iTRAQ comparison experiments, and according to the criterion of signification for continuous characters [ 41 , 42 ], such that 0 is down-regulated and 1 is an up-regulated protein [ 35 ]. Only proteins that were identified in all biological replicates showing some significant values were accepted.…”

“…Limited results have been known on expressed proteome differences regarding any species of this important parasitic nematode genus. Because comparison of protein expression profiles can be treated as quantitative inheritance characters [ 33 ], its codification in discrete states would facilitate the finding of unambiguous proteins markers with taxonomic, evolutionary and phylogenetic value [ 29 , 34 , 35 ]. Here, we applied these assumptions as a proteomic discovery phase [ 27 ] to three Anisakis taxonomic entities ( A. simplex s.s., A. pegreffii , and their hybrid genotype) in order to characterize and select a unique set of specific proteins as taxonomic markers able to be experimentally targeted (qualification, verification, validation) and also to provide a methodological framework focusing on taxonomical protein markers of other species of the genus Anisakis for clinical and food diagnostic purposes.…”

BRC4Env, a network of Biological Resource Centres for research in environmental and agricultural sciences

“…For example, the pinewood nematode collection has been instrumental in the achievement of some objectives of the FP7/EU-project REPHRAME (Development of improved methods for detection, control and eradication of pine wood nematode in support of EU Plant Health Policy). Together with additional field sampling, these biological resources have been used to characterize the genetic diversity of nematode populations from both the native and the invaded areas, and to infer the worldwide routes of invasion of the parasite (Vieira et al 2014 ; Mallez et al 2015 ; Ciordia et al 2016 ). These new data are of direct practical importance for the implementation of efficient phytosanitary measures for quarantine regulation.…”