Quantitative proteomics links metabolic pathways to specific developmental stages of the plant-pathogenic oomycete Phytophthora capsici

Family 92 carbohydrate-binding modules specific for β-1,6-glucans increase the thermostability of a bacterial chitinase

In biomass-processing industries there is a need for enzymes that can withstand high temperatures. Extensive research efforts have been dedicated to finding new thermostable enzymes as well as developing new means of stabilising existing enzymes. The attachment of a stable non-catalytic domain to an enzyme can, in some instances, protect a biocatalyst from thermal denaturation. Carbohydrate-binding modules (CBMs) are non-catalytic domains typically found appended to biomass-degrading or modifying enzymes, such as glycoside hydrolases (GHs). Most often, CBMs interact with the same polysaccharide as their enzyme partners, leading to an enhanced reaction rate via the promotion of enzyme-substrate interactions. Contradictory to this general concept, we show an example of a chitin-degrading enzyme from GH family 18 that is appended to two CBM domains from family 92, both of which bind preferentially to the non-substrate polysaccharide β-1,6-glucan. During chitin hydrolysis, the CBMs do not contribute to enzyme-substrate interactions but instead confer a 10-15 °C increase in enzyme thermal stability. We propose that CBM92 domains may have a natural enzyme stabilisation role in some cases, which may be relevant to enzyme design for high-temperature applications in biorefinery.

Synthesis of aglycones, structure-activity relationships, and mode of action of lycosides as inhibitors of the asexual reproduction of Phytophthora

Phytophthora are plant pathogens that damage agricultural products. Lycosides (1a-d), found in vegetable juice, have the potential to curb the rapid outbreak and crop damage caused by the asexual reproduction of Phytophthora. Here, aglycones 2a, b with slightly higher activity than lycosides were synthesized as a diastereomeric mixture (mix-2) possessing activity (IC50 = 4.1 µm) comparable with that of lycosides. The importance of the cyclohexanone structure and side-chain length was demonstrated via structure-activity relationship analysis using synthetic intermediates. In addition, the action mechanism of lycosides was investigated using transcriptome analysis, which revealed a contribution to proline biosynthesis inhibition, a process crucial for the asexual reproduction of Phytophthora. These findings indicate that lycosides (and aglycone) are environmentally benign agents that can be used for protecting agricultural products from Phytophthora pathogens.

Molecular sensors reveal the mechano-chemical response of Phytophthora infestans walls and membranes to mechanical and chemical stress

Phytophthora infestans, causal agent of late blight in potato and tomato, remains challenging to control. Unravelling its biomechanics of host invasion, and its response to mechanical and chemical stress, could provide new handles to combat this devastating pathogen. Here we introduce two fluorescent molecular sensors, CWP-BDP and NR12S, that reveal the micromechanical response of the cell wall-plasma membrane continuum in P. infestans during invasive growth and upon chemical treatment. When visualized by live-cell imaging, CWP-BDP reports changes in cell wall (CW) porosity while NR12S reports variations in chemical polarity and lipid order in the plasma membrane (PM). During invasive growth, mechanical interactions between the pathogen and a surface reveal clear and localized changes in the structure of the CW. Moreover, the molecular sensors can reveal the effect of chemical treatment to CW and/or PM, thereby revealing the site-of-action of crop protection agents. This mechano-chemical imaging strategy resolves, non-invasively and with high spatio-temporal resolution, how the CW-PM continuum adapts and responds to abiotic stress, and provides information on the dynamics and location of cellular stress responses for which, to date, no other methods are available.

Comparative proteomics reveals biochemical changes in Salvia miltiorrhiza Bunge during sweating processing

ETHNOPHARMACOLOGICAL RELEVANCE

Salvia miltiorrhiza Bunge is a bulk medicinal material used in traditional Chinese medicine, that can cure cardiovascular diseases, neurasthenia, and other conditions. Sweating is a frequently used method of processing S. miltiorrhiza for medical applications. We previously demonstrated changes to the metabolic profile of linoleic acid, glyoxylate, and dicarboxylate after Sweating. However, this alteration has not been explained at the molecular level.

MATERIALS AND METHODS

Fresh roots of Salvia miltiorrhiza Bunge were treated by the Sweating processing, and then the tandem mass tag technique was used to compare the proteome difference between Sweating S. miltiorrhiza and non-Sweating S. miltiorrhiza.

RESULTS

We identified a total of 850 differentially expressed proteins after Sweating treatment in S. miltiorrhiza, including 529 upregulated proteins and 321 downregulated proteins. GO enrichment analysis indicated that these differentially expressed proteins are involved in external encapsulating structure, cell wall, oxidoreductase activity, ligase activity, and others. Further analysis showed that CYP450, the pathogenesis-related protein Bet v 1 family, and the peroxidase domain were the major protein domains. KEGG enrichment identified 18 pathways, of which phenylpropanoid biosynthesis is the most important one related to the metabolite profile and is the principal chemical component of S. miltiorrhiza.

CONCLUSION

This study addressed potential molecular mechanisms in S. miltiorrhiza after Sweating, and the findings provide reasons for the changes in biochemical properties and metabolites changes which might cause pharmacological variation at the proteome level.

iTRAQ proteomic analysis of the inhibitory effect of 1,6-O,O-diacetylbritannilactone on the plant pathogenic oomycete Phytophthora capsici

Phytophthora capsici is a highly destructive oomycete of vegetables; its management is challenging due to its broad host range, rapid dispersion, resilient spores and severe fungicide resistance. Identifying an effective alternative fungicide is important for the control of P. capsici. 1,6-O,O-diacetylbritannilactone (ABLOO), one of the secondary metabolites of Inula Britannica, showed a favorable inhibitory activity against P. capsici at different developmental stages, with a sensitivity order as follows: sporangia formation (30.45 mg/L) > zoospore discharge (77.69 mg/L) > mycelial growth (93.18 mg/L) > cystospore germination (591.48 mg/L). To investigate the mode of action of ABLOO in P. capsici, iTRAQ-based quantitative proteomic analysis was performed by comparing the expression levels of proteins in the control and ABLOO-treated (400 mg/L, inhibition rate of 80%) mycelial groups. A total of 65 downregulated and 75 upregulated proteins were identified in the proteomic analysis. Functional enrichment analyses showed that proteins with transmembrane transport activity were significantly inhibited, while proteins involved in energy production were significantly increased, including proteins involved in ubiquinone and other terpenoid-quinone biosynthesis, oxidative phosphorylation, and glycolysis/gluconeogenesis. The morphological results indicated that ABLOO treatment could decrease the thickness of the cell walls of P. capsici mycelia. Correspondingly, biochemical results showed that ABLOO treatment reduced the β-1,3-glucan contents (the key component of the cell wall of P. capsici) and increased the cell membrane permeability of P. capsici. ABLOO may exhibit antioomycete activity by destroying the cell membrane of P. capsici. This study provides new evidence regarding the inhibitory mechanisms of ABLOO against P. capsici.

Phytophthora capsici sterol reductase PcDHCR7 has a role in mycelium development and pathogenicity

The de novo biosynthesis of sterols is critical for the majority of eukaryotes; however, some organisms lack this pathway, including most oomycetes. Phytophthora spp. are sterol auxotrophic but, remarkably, have retained a few genes encoding enzymes in the sterol biosynthesis pathway. Here, we show that PcDHCR7, a gene in Phytophthora capsici predicted to encode Δ7-sterol reductase, displays multiple functions. When expressed in Saccharomyces cerevisiae, PcDHCR7 showed the Δ7-sterol reductase activity. Knocking out PcDHCR7 in P. capsici resulted in loss of the capacity to transform ergosterol into brassicasterol, which means PcDHCR7 has the Δ7-sterol reductase activity in P. capsici itself. This enables P. capsici to transform sterols recruited from the environment for better use. The biological characteristics of ΔPcDHCR7 transformants were compared with those of the wild-type strain and a PcDHCR7 complemented transformant, and the results showed that PcDHCR7 plays a key role in mycelium development and pathogenicity of zoospores. Further analysis of the transcriptome indicated that the expression of many genes changed in the ΔPcDHCR7 transformant, which involve in different biological processes. It is possible that P. capsici compensates for the defects caused by the loss of PcDHCR7 by remodelling its transcriptome.

In Planta Transcriptome and Proteome Profiles of Spongospora subterranea in Resistant and Susceptible Host Environments Illuminates Regulatory Principles Underlying Host-Pathogen Interaction

Simple Summary

Infections of potato tubers and roots by Spongospora subterranea result in powdery scab and root diseases. Losses due to infections with S. subterranea are substantial in most potato-growing regions of the world with no fully effective treatments available. Understanding the gene regulation of pathogens in their host is dependent on multidimensional datasets. In this study, we profiled the transcriptome and proteome of S. subterranea within the susceptible and resistant host. Enzyme activity and nucleic acid metabolism appear to be important to the virulence of S. subterranea. Our results provide a good resource for future functional studies of powdery scab and might be useful in S. subterranea inoculum management.

Abstract

Spongospora subterranea is an obligate biotrophic pathogen, causing substantial economic loss to potato industries globally. Currently, there are no fully effective management strategies for the control of potato diseases caused by S. subterranea. To further our understanding of S. subterranea biology during infection, we characterized the transcriptome and proteome of the pathogen during the invasion of roots of a susceptible and a resistant potato cultivar. A total of 7650 transcripts from S. subterranea were identified in the transcriptome analysis in which 1377 transcripts were differentially expressed between two cultivars. In proteome analysis, we identified 117 proteins with 42 proteins significantly changed in comparisons between resistant and susceptible cultivars. The functional annotation of transcriptome data indicated that the gene ontology terms related to the transportation and actin processes were induced in the resistant cultivar. The downregulation of enzyme activity and nucleic acid metabolism in the resistant cultivar suggests a probable influence of these processes in the virulence of S. subterranea. The protein analysis results indicated that the majority of differentially expressed proteins were related to the metabolic processes and transporter activity. The present study provides a comprehensive molecular insight into the multiple layers of gene regulation that contribute to S. subterranea infection and development in planta and illuminates the role of host immunity in affecting pathogen responses.

Quantitative proteomics provides an insight into germination-related proteins in the obligate biotrophic plant pathogen Spongospora subterranea

The soil-borne and obligate plant-associated nature of S. subterranea has hindered a detailed study of this pathogen and in particular, the regulatory pathways driving the germination of S. subterranea remain unknown. To better understand the mechanisms that control the transition from dormancy to germination, protein profiles between dormant and germination stimulant-treated resting spores were compared using label-free quantitative proteomics. Among the ~680 proteins identified 20 proteins were found to be differentially expressed during the germination of S. subterranea resting spores. Elongation factor Tu, histones (H2A and H15), proteasome and DJ-1_PfpI, involved in transcription and translation, were upregulated during the germination of resting spores. Downregulation of both actin and beta-tubulin proteins occurred in the germinating spores, indicating that the changes in the cell wall cytoskeleton may be necessary for the morphological changes during the germination of the resting spore in S. subterranea. Our findings provide new approaches for the study of these and similar recalcitrant micro-organisms provide the first insights into the basic protein components of S. subterranea spores. A better understanding of S. subterranea biology may lead to the development of novel approaches for the management of persistent soil inoculum.

The consensus Nglyco -X-S/T motif and a previously unknown Nglyco -N-linked glycosylation are necessary for growth and pathogenicity of Phytophthora

Asparagine (Asn, N)-linked glycosylation within N_glyco -X-S/T; X ≠ P motif is a ubiquitously distributed post-translational modification that participates in diverse cellular processes. In this work, N-glycosylation inhibitor was shown to prevent Phytophthora sojae growth, suggesting that N-glycosylation is necessary for oomycete development. We conducted a glycoproteomic analysis of P. sojae to identify and map N-glycosylated proteins and to quantify differentially expressed glycoproteins associated with mycelia, asexual cyst, and sexual oospore developmental stages. A total of 355 N-glycosylated proteins was found, containing 496 glycosites, potentially involved in glycan degradation, carbon metabolism, glycolysis, or other metabolic pathways. Through PNGase F deglycosylation assays and site-directed mutagenesis of a GPI transamidase protein (GPI16) upregulated in cysts and a heat shock protein 70 (HSP70) upregulated in oospores, we demonstrated that both proteins were N-glycosylated and that the N_glyco -N motif is a target site for asparagine - oligosaccharide linkage. Glycosite mutations of Asn 94 N_glyco -X-S/T in the GPI16 led to impaired cyst germination and pathogenicity, while mutation of the previously unknown Asn 270 N_glyco -N motif in HSP70 led to decreased oospore production. In addition to providing a map of the oomycete N-glycoproteome, this work confirms that P. sojae has evolved multiple N-glycosylation motifs essential for growth.

Proteomics Reveals the Mechanism Underlying the Inhibition of Phytophthora sojae by Propyl Gallate

Phytophthora sojae is a serious soil-borne pathogen, and the major control measures undertaken include the induction of soybean-resistance genes, fungicides, and scientific and reasonable planting management. Owing to the safety and resistance of fungicides, it is of great importance to screen new control alternatives. In a preliminary study, we observed that propyl gallate (PG) exerts a considerable inhibitory effect on P. sojae and can effectively prevent and cure soybean diseases, although the underlying mechanism remains unclear. To explore the inhibitory mechanism of PG on P. sojae, we analyzed the differences in the protein profile of P. sojae before and after treatment with PG using tandem mass tag (TMT) proteomics. Proteomic analysis revealed that the number of differentially expressed proteins (DEPs) was 285, of which 75 were upregulated and 210 were downregulated, and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways primarily comprised glycolysis, tricarboxylic acid cycle, fatty acid metabolism, secondary metabolite generation, and other pathways. Among the DEPs involved in PG inhibition of P. sojae are two closely related uncharacterized proteins encoded by PHYSODRAFT_522340 and PHYSODRAFT_344464, denoted PsFACL and PsCPT herein. The CRISPR/Cas9 knockout technique revealed that PsFACL and PsCPT were involved in the growth rate and pathogenicity. In addition, the results of gas chromatography-mass spectrometry (GC-MS) showed that there were differences in fatty acid levels between wild-type (WT) and CRISPR/Cas9 knockout transformants. Knocking out PsFACL and PsCPT resulted in the restriction of the synthesis and β-oxidation of long-chain fatty acids, respectively. These suggest that PsFACL and PsCPT were also involved in the regulation of the fatty acid metabolism. Our results aid in understanding the mechanism underlying the inhibition of P. sojae growth by PG.

Identification of differentially activated pathways in Phytophthora sojae at the mycelial, cyst, and oospore stages by TMT-based quantitative proteomics analysis

Phytophthora sojae is a widely distributed, destructive oomycete plant pathogen that has been developed as a model for oomycete biology. Given the important but limited reports on the comparison of the sexual and asexual stages in Phytophthora, we performed a large-scale quantitative proteomics study on two key asexual life stages of P. sojae-the mycelium and cyst-as well as on the oospore, which is a key sexual stage. Over 29,631 peptides from 4688 proteins were analyzed. Briefly, 445 proteins, 624 proteins, and 579 proteins were defined as differentially quantified proteins in cyst vs mycelium, oospore vs cyst, and oospore vs mycelium comparisons, respectively (|log2 fold change| > 1 and P < 0.05). Compared to the mycelium and oospore, fatty acid and nitrogen metabolism were specifically induced in cysts. In oospores, the up-regulated proteins focused on RNA transport and protein processing in endoplasmic reticulum, indicating translation, folding, and the secretion of core cellular or stage-specific proteins active in oospores, which might be used for oospore germination. The data presented expand our knowledge of pathways specifically linked to asexual and sexual stages of this pathogen. BIOLOGICAL SIGNIFICANCE: The sexual spores (oospores) in oomycetes have thick cell walls and can survive in the soil for years, thus providing a primary source and allowing the reinfection of their host plant in subsequent growing seasons. However, the proteomic study on oospores remains very limited as they are generally considered to be dormant. In the present study, we successfully isolated oospores, and performed a large-scale comparative quantitative proteomics study on this key sexual stage and two representative asexual stages of P. sojae. The results provide an improved understanding of P. sojae biology and suggest potential metabolic targets for disease control at the three different developmental stages in oomycetes.

Quantitative Proteomic Analysis of Four Developmental Stages of Saprolegnia parasitica

Several water mold species from the Saprolegnia genus infect fish, amphibians, and crustaceans in natural ecosystems and aquaculture farms. Saprolegnia parasitica is one of the most severe fish pathogens. It is responsible for millions of dollars of losses to the aquaculture industry worldwide. Here, we have performed a proteomic analysis, using gel-based and solution (iTRAQ) approaches, of four defined developmental stages of S. parasitica grown in vitro, i.e., the mycelium, primary cysts, secondary cysts and germinated cysts, to gain greater insight into the types of proteins linked to the different stages. A relatively high number of kinases as well as virulence proteins, including the ricin B lectin, disintegrins, and proteases were identified in the S. parasitica proteome. Many proteins associated with various biological processes were significantly enriched in different life cycle stages of S. parasitica. Compared to the mycelium, most of the proteins in the different cyst stages showed similar enrichment patterns and were mainly related to energy metabolism, signal transduction, protein synthesis, and post-translational modifications. The proteins most enriched in the mycelium compared to the cyst stages were associated with amino acid metabolism, carbohydrate metabolism, and mitochondrial energy production. The data presented expand our knowledge of metabolic pathways specifically linked to each developmental stage of this pathogen.

RNA-seq of life stages of the oomycete Phytophthora infestans reveals dynamic changes in metabolic, signal transduction, and pathogenesis genes and a major role for calcium signaling in development

BACKGROUND

The oomycete Phytophthora infestans causes the devastating late blight diseases of potato and tomato. P. infestans uses spores for dissemination and infection, like many other filamentous eukaryotic plant pathogens. The expression of a subset of its genes during spore formation and germination were studied previously, but comprehensive genome-wide data have not been available.

RESULTS

RNA-seq was used to profile hyphae, sporangia, sporangia undergoing zoosporogenesis, motile zoospores, and germinated cysts of P. infestans. Parallel studies of two isolates generated robust expression calls for 16,000 of 17,797 predicted genes, with about 250 transcribed in one isolate but not the other. The largest changes occurred in the transition from hyphae to sporangia, when >4200 genes were up-regulated. More than 1350 of these were induced >100-fold, accounting for 26% of total mRNA. Genes encoding calcium-binding proteins, cation channels, signaling proteins, and flagellar proteins were over-represented in genes up-regulated in sporangia. Proteins associated with pathogenicity were transcribed in waves with subclasses induced during zoosporogenesis, in zoospores, or in germinated cysts. Genes involved in most metabolic pathways were down-regulated upon sporulation and reactivated during cyst germination, although there were exceptions such as DNA replication, where transcripts peaked in zoospores. Inhibitor studies indicated that the transcription of two-thirds of genes induced during zoosporogenesis relied on calcium signaling. A sporulation-induced protein kinase was shown to bind a constitutive Gβ-like protein, which contributed to fitness based on knock-down analysis.

CONCLUSIONS

Spore formation and germination involves the staged expression of a large subset of the transcriptome, commensurate with the importance of spores in the life cycle. A comparison of the RNA-seq results with the older microarray data indicated that information is now available for about twice the number of genes than before. Analyses based on function revealed dynamic changes in genes involved in pathogenicity, metabolism, and signaling, with diversity in expression observed within members of multigene families and between isolates. The effects of calcium signaling, a spore-induced protein kinase, and an interacting Gβ-like protein were also demonstrated experimentally. The results reveal aspects of oomycete biology that underly their success as pathogens and potential targets for crop protection chemicals.