The proximity interactome of the peach-potato aphid (Myzus persicae) cathepsin B in Arabidopsis thaliana

Introduction

In agriculture, the peach-potato aphid Myzus persicae (Sulzer) has one of the broadest host ranges among insects and cause devastating crop losses worldwide (CABI, 2022). They are highly adaptable, displaying a wide range of plastic responses to environmental cues, including the ability to develop as either winged or wingless forms and to reproduce through either asexual or sexual means (Brisson, 2010; Ogawa and Miura, 2014; Grantham and Brisson, 2018). Remarkably, M. persicae differentially regulate the transcription of certain gene clusters to facilitate colonization of diverse plant species (Mathers et al., 2017; Chen et al., 2020). Among these gene clusters are members of the cysteine protease family, cathepsin B (CathB).

Host responsive CathB genes are organized in tandemly repeated clusters in the M. persicae genome and belong to a recently expanded clade in phylogeny (Mathers et al., 2017). They are upregulated when aphids feed on Arabidopsis thaliana and Brassica rapa and knock down of their expression using RNA interference reduces aphid reproduction on A. thaliana (Chen et al., 2020). Intriguingly, peptides corresponding to CathB proteins are detected in M. persicae oral secretion (OS), indicating that at least some CathB proteins are directly delivered into plant cells during aphid feeding (Guo et al., 2020; Liu et al., 2024).

Among M. persicae CathB proteins, CathB6 is most highly expressed in aphids on A. thaliana (Chen et al., 2020) and most abundant in M. persicae OS (Liu et al., 2024). To identify the potential plant targets of M. persicae CathB, we optimized the TurboID-based proximity labelling and MS (PL-MS) protocol (Fig. 1).

As a first step, we generated stable transgenic A. thaliana lines producing GFP or CathB6 as C-terminal TurboID-3×FLAG fusions (GFP-TurboID or CathB6-TurboID). Seedlings of these plants were treated with biotin followed by affinity capture with streptavidin beads (Fig. 2A). Enrichment of biotinylated proteins was confirmed by western blotting (Fig. 2B), followed by nanoLC-MS/MS analyses.

Principal component analysis (PCA) of the MS data showed that the three CathB6-TurboID samples were grouped together, separately from three GFP-TurboID samples (Fig. 2C). Furthermore, MA plot confirmed that the CathB6-TurboID and GFP-TurboID samples are distinct (Fig. 2D). From the complete dataset, 267 A. thaliana proteins exhibited statistically significant enrichment (p-value < 0.05) of more than 2-fold and were consistently identified in at least two replicates of the CathB6-TurboID samples compared to the GFP-TurboID controls (Fig. 2E, Table 1). This compares to 223 proteins in the GFP-TurboID samples versus CathB6-TurboID samples (Fig. 2E, Table 1). Additionally, we identified 20 unique peptides corresponding to CathB6 in the CathB6-TurboID samples and 19 unique peptides corresponding to GFP in the GFP-TurboID samples (Table 1). These data suggest that this PL-MS protocol worked dnd identified genuine interactors of CathB6.

Together, this dataset identifies 267 potential plant interactors of aphid CathB6, which may contribute to CathB6 modulation of A. thaliana plant for colonization. Further mechanistic studies should be done to characterize if these potential interactors are involved and how the relevant pathways are affected after CathB delivery through aphid feeding.

Materials and Methods

Plasmid construction

For the construction of plasmids producing CathB6-TurboID-3×FLAG, the coding sequences corresponding to the catalytic domain (without signal peptide and prodomain regions) of CathB6 (Arg61-Asn338) and TurboID-3×FLAG were separately amplified. Then, the two fragments were connected using overlap PCR (Nelson and Fitch, 2011). After cloning of the sequence corresponding to the CathB6-TurboID-3×FLAG fragment into the pJET vector and sequencing, CathB6-TurboID-3×FLAG was amplified with primers containing attB extensions and cloned into the pDONOR207 vector, followed by the ligation to Gateway destination vector pB7WG2 containing a 35S promoter. Similar cloning methods were used for construction of GFP-TurboID-3×FLAG.

Plant transformation

The constructed plasmids were introduced into Agrobacterium tumefaciens strain GV3101, and the cultures were grown on plates at 28 °C for 24–48 hrs. Then, positive colonies were identified via PCR using plasmids extracted from overnight liquid cultures and gene-specific primers. Positive colonies were grown at 28 °C in liquid cultures and transformed into A. thaliana Col-0 plants using the floral dipping method (Bechtold, 1993). Transgenic seeds were harvested and selected on Murashige and Skoog (MS) medium supplemented with 20 μg/mL phosphinothricin (BASTA) and screened for ratio of 3:1 alive/dead segregation. After screening for two or three generations, transgenic plants were deemed to harbor single homozygous transgenes and were used for proximity labeling once germinated seeds achieved a 100% survival rate.

Proximity labelling

Seeds of A. thaliana plants stably expressing GFP-TurboID-3×FLAG or CathB6-TurboID-3×FLAG were sowed on ½ MS plates containing 1.0% sucrose and 0.3% phytagel and placed under long-day condition (16 h light/8 h dark) at 22 °C. After 10 days, 2.5 g seedlings were collected and submerged in 50 µM biotin solution for 4 hrs at RT. Afterwards, seedlings were rinsed with ice-cold MilliQ water for 5 times. After removing excess liquid with paper towel, seedings were ground with pestle, mortar and nitrogen to a fine powder. Protein extraction was performed in 5 mL of extraction buffer [150 mM Tris-HCl (pH 7.5), 150 mM NaCl, 1 mM EDTA, 10% Glycerol, 10 mM DTT, 0.4% Nonidet-40, 0.1% (w/v) Deoxycholic acid, 2% (w/v) PVPP, 1 tablet of cOmplete protease Inhibitor cocktail (Roche, Catalog number 10697498001)] and incubation on a rotor wheel at 4 °C for 30 min, followed by centrifugation of the tubes at 5000 g for 15 min to remove the cell debris. The upper soluble fraction was then run through the Zeba Spin Desalting Column (Thermo Fisher Scientific, Catalog number 89893) to remove excess biotin from the lysates. Fifty (50) µL of desalted lystate was used as input for western blot analysis, while the rest of the desalted lysate was incubated with High Capacity Streptavidin Agarose Resin (Thermo Fisher Scientific, Catalog number 20361) on a rotor wheel at 4 °C overnight. The next day, Streptavidin beads were sequentially washed once in 1 mL Buffer 1 (2% SDS in water), once in 1 mL Buffer 2 [150 mM Tris-HCl (pH 7.5), 150 mM NaCl, 1 mM EDTA, 10% Glycerol, 0.1% (w/v) Deoxycholic acid (w/v), 1% Triton X-100], once in buffer 3 [10 mM Tris-HCl (pH 7.4), 250 mM LiCl, 1 mM EDTA, 0.1% (w/v) Deoxycholic acid, 1% (v/v) NP40], twice in Buffer 4 [50mM Tris-HCl (pH 7.5)], and six times in Buffer 5 (50mM ammonium bicarbonate, pH 8.0). Finally, the streptavidin beads were resuspended in 200 µL of 50 mM ammonium bicarbonate. For quality control of the TurboID immunoprecipitation, 10% (20 µL) of the suspension was taken out for Western blot analysis, and the remaining bead suspension was flash-frozen in liquid nitrogen and stored at -80 °C and submitted to nano LC-MS/MS analysis.

For western blot analysis, 20 µL of suspended streptavidin beads in washing buffer 5 were added to 10 µL of 4× LDS Sample Loading Buffer, 10 mM DTT and 2 mM biotin, and boiled for 10 min. Samples were loaded onto 12% SDS-PAGE gels (Invitrogen) and transferred to 0.22 μm PVDF membranes using the Bio-Rad mini-PROTEAN Electrophoresis system. Membranes were hybridized with Streptavidin-HRP.

NanoLC-MS/MS

 Biotinylated proteins enriched with streptavidin beads were processed with trypsin via on bead digestion. The beads were washed in water and resuspended in of 1.5% sodium deoxycholate (SDC; Merck) in 0.2 M EPPS-buffer (Merck) to 50% bead slurry vol/vol, pH 8.5 and vortexed under heating. Cysteine residues were reduced with dithiothreitol, alkylated with iodoacetamide, and the proteins digested with trypsin in the SDC buffer according to standard procedures for 8 hrs. The beads were then pelleted by centrifugation and the supernatant was collected for SDC precipitation by adding trifluoroacetic acid (TFA) to a final concentration of 0.2%. The clear supernatant was subjected to C18 SPE using home-made stage tips with C18 Reprosil_pur 120, 5 µm (Dr. Maisch GmbH, Germany). Aliquots were analyzed by nano LC-MS/MS on an Orbitrap Eclipse™ Tribrid™ mass spectrometer equipped with a FAIMS Pro Duo interface coupled to an UltiMate® 3000 RSLC nano LC system (Thermo Fisher Scientific, Hemel Hempstead, UK). The samples were loaded onto a trap cartridge (PepMap™ Neo Trap Cartridge, C18, 5um, 0.3x5mm, Thermo) with 0.1% TFA at 15 µl min-1 for 3 min. The trap column was then switched in-line with the analytical column (Aurora Frontier TS, 60 cm nanoflow UHPLC column, ID 75 µm, reversed phase C18, 1.7 µm, 120 Å; IonOpticks, Fitzroy, Australia) for separation at 55°C using the following gradient of solvents: A (water, 0.1% formic acid) and B (80% acetonitrile, 0.1% formic acid) at a flow rate of 0.26 µl min-1 : 0-3 min 1% B (parallel to trapping); 3-10 min increase B (curve 4) to 8%; 10-102 min linear increase B to 48; followed by a ramp to 99% B and re-equilibration to 0% B. Total runtime was 140 min.

Mass spectrometry data were acquired between 10 and 110 min with the FAIMS device set to three compensation voltages (-35V, -50V, -65V) at standard resolution for 1.0 s each with the following MS settings in positive ion mode: OT resolution 120K, profile mode, mass range m/z 300-1600, normalized AGC target 100%, max inject time 50 ms; MS2 in IT Turbo mode: quadrupole isolation window 1 Da, charge states 2-5, threshold 1e4, HCD CE = 30, AGC target standard, max. injection time dynamic, dynamic exclusion 1 count for 15 s with mass tolerance of ±10 ppm, one charge state per precursor only.

The mass spectrometry raw data were processed and quantified in Proteome Discoverer 3.1 (PD3.1) (Thermo) using the search engine CHIMERYS (MSAID, Munich, Germany); all mentioned tools of the following workflow are nodes of the proprietary Proteome Discoverer (PD) software. The A. thaliana protein sequence database (TAIR10, 35,386 entries, from 14/12/2010), the two sequences of the used TurboID constructs, and the MaxQuant contaminants database (240812, 246 entries) were imported into PD adding a reversed sequence database for decoy searches.

The database search was performed using the search engine CHIMERYS (MSAID, Munich, Germany). The processing workflow started with spectrum recalibration, Minora Feature Detection with min. trace length 5, S/N 2.5, PSM confidence high, and Top N Peak Filter with 20 peaks per 100 Da. For CHIMERYS, the inferys_3.0.0_fragmentation prediction model with FDR targets 0.01 (strict) and 0.05 (relaxed), a fragment tolerance of 0.3 Da, enzyme trypsin with 2 missed cleavages, variable modification oxidation (M), fixed modification carbamidomethyl (C) were used.

The consensus workflow in the PD3.1 software was used to evaluate the peptide identifications and to measure the abundances of the peptides based on the LC-peak intensities. For chromatographic alignment and feature mapping, a retention time tolerance of 2 min, a mass tolerance of 1 ppm, and an S/N threshold of 5 were used. For quantification, three replicates per condition were measured. In PD3.1, the following parameters were used for ratio calculation: normalization on total peptide abundances, protein abundance-based ratio calculation using the Top3 most abundant peptides, missing values imputation by low abundance resampling, hypothesis testing by t-test (background based), adjusted p-value calculation by BH-method.  The results were exported into a Microsoft Excel table including data for protein abundances, ratios, p-values, number of peptides, protein coverage, the CHIMERYS identification score and other important values.

Data availability statement

The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier with the dataset identifier PXD057789 and 10.6019/PXD057789.

Acknowledgements

 This research was funded by UK Research and Innovation (UKRI) Biotechnology and Biological Sciences Research Council (BBSRC) grants to SAH (BB/V008544/1 and BB/R009481/1). Additional Support is provided by the BBSRC Institute Strategy Programmes (BBS/E/J/000PR9797 and BBS/E/JI/230001B) awarded to the JIC. The JIC is grant-aided by the John Innes Foundation.

Conflicts of Interest

 The authors declare that no conflicts of interest exist.

Legends of figures and tables

Figure 1. Principle of CathB6-TurboID based proximity labelling with MS (PL-MS). The TurboID biotin ligase (TurboID) is fused to C-terminus of CathB6. Exogenous addition of biotin (yellow stars) biotinylates proteins in the proximity of CathB6-TurboID fusion protein, whereas distal proteins are not biotinylated. The biotinylated proteins are captured by incubating total proteins extracts with streptavidin beads. Peptides derived from biotinylated proteins, most of which are in the proximity of CathB6-TurboID, are detected by nanoLC-MS.

Fig. 2. Sample preparation and quantification for CathB6-TurboID interactome in A. thaliana. (A) Sample preparation working flow for TurboID-based proximity labeling. GFP-TurboID and CathB6-TurboID seedlings were treated with 50 µM biotin for 4 hrs at room temperature. (B) Visualization on western blots of biotinylated proteins detected after desalting step (input) and 12 wash steps of Streptavidin beads (Streptavidin IP) as per workflow shown in (A). (C) Principal component analysis (PCA) of three replicates of GFP-TurboID and CathB6-TurboID samples. (D) MA plot of three replicates of GFP-TurboID and CathB6-TurboID samples. (E) Venn diagrams showing the overlap of proteins identified in three biological replicates of GFP-TurboID (left) and CathB6-TurboID (right) upon a fold-change of CathB6-TurboID/GFP-TurboID > 2, n = 267. 

Table 1. Full list of proteins detected from CathB6-TurboID PL-MS.

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