Mutations in the Membrane-Anchored SdhC Subunit Affect Fitness and Sensitivity to Succinate Dehydrogenase Inhibitors in Botrytis cinerea Populations from Multiple Hosts

Exploring SDHI fungicide resistance in Botrytis cinerea through genetic transformation system and AlphaFold model-based molecular docking

BACKGROUND

Gray mold caused by Botrytis cinerea is one of the most serious diseases affecting strawberry. Succinate dehydrogenase inhibitor (SDHI) fungicides have been used for more than a decade to control the disease. Monitoring resistance and improving in-depth understanding of resistance mechanisms are essential for the control of B. cinerea.

RESULTS

In this study, resistance monitoring of a SDHI fungicide boscalid was conducted on B. cinerea isolated from strawberries in Korea during 2020 and 2021, with resistance rates of 76.92% and 72.25%, respectively. In resistant strains, mutations P225F/H and H272R were found in SdhB, with P225F representing the dominant mutation type. Simultaneous mutations G85A, I93V, M158V, and V168I in SdhC were detected in 54.84% of sensitive strains. Sensitivity profiles of different Sdh genotypes of B. cinerea strains to six SDHIs were determined in vitro and in vivo. In addition, the mutation(s) were genetically validated through in situ SdhB (SdhC) expression. Docking assays between SDHIs and AlphaFold model-based Sdh complexes revealed generally consistent patterns with their in vitro phenotypes.

CONCLUSION

Resistance of B. cinerea to SDHI fungicide on strawberry was systematically investigated in this study. Deciphering of SDHI resistance through the genetic transformation system and AlphaFold model-based molecular docking will provide valuable insights into other target site-based fungicide resistance in fungal pathogens. © 2024 The Author(s). Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Genotypic and phenotypic characterization of resistance to fenhexamid, carboxin, and, prochloraz, in Botrytis cinerea isolates collected from cut roses in Colombia

Gray mold, caused by Botrytis sp., is a significant disease in Colombian rose crops and its control depends primarily on the intensive use of chemically synthesized fungicides. Despite the importance of this pathogen, there is limited information in Colombian floriculture about molecular taxonomy of species, fungicide resistance of populations and their genetic mechanism of resistance. In this study, we analyze 12 isolates of this fungus collected from rose-producing crops in the Department of Cundinamarca and conducted phylogenetic analysis using HSP60, G3PDH, and RPB2 gene sequences. Additionally, we realize phenotypic and genotypic characterization of resistance to the fungicides fenhexamid, carboxin, and prochloraz, evaluating the in vitro EC50 and presence of mutations of target genes of each isolate. All isolates were characterized as Botrytis cinerea in the phylogenetic analysis and presents different levels of resistance to each fungicide. These levels are related to mutations in target genes, with predominancy of L195F and L400F in the ERG27 gene to fenhexamid resistance, H272R/Y in the SDHB gene for carboxin resistance, and Y136F in the CYP51 gene for prochloraz resistance. Finally, these mutations were not related to morphological changes. Collectively, this knowledge, presented for the first time to the Colombian floriculture, contribute to a better understanding of the genetic diversity and population of B. cinerea from rose-producing crops in the department of Cundinamarca, and serve as a valuable tool for making informed decisions regarding disease management, future research, and improving crop management and sustainability in the Colombian floriculture industry.

Subcellular biochemistry and biology of filamentous entomopathogenic fungi

Filamentous entomopathogenic fungi (EPF) function as important biotic factors regulating the arthropod population in natural ecosystems and have great potential as biocontrol agents in modern agriculture. In the infection cycle, EPF undergo a plethora of physiological processes, including metabolism (e.g., cuticle hydrolysis and nutrient utilization), development (e.g., dimorphism and conidiation), stress response (e.g., oxidative and osmotic stresses), and immune evasion from the host. In-depth explorations of the mechanisms involved in the lifecycle of EPF offer excellent opportunities to increase their virulence and stability, which increases the efficacy of EPF in biocontrol programs. This review discusses the current state of knowledge relating to the biological roles and regulatory mechanisms of organelles and subcellular structures in the physiology of EPF, as well as some suggestions for future investigation.

Resistance of the Ginseng Gray Mold Pathogen, Botrytis cinerea, to Boscalid and Pyraclostrobin Fungicides in China

Gray mold caused by Botrytis cinerea severely threatens the yield of ginseng (Panax ginseng). Various categories of fungicides have been utilized to control gray mold on this crop. In this study, the resistance of 102 isolates of B. cinerea from 11 commercial ginseng-growing regions in China to fungicides was examined. A total of 32.4% were resistant to boscalid, with EC50 values that ranged from 12.26 to 235.87 μg/ml, and 94.1% were resistant to pyraclostrobin, with EC50 values that ranged from 5.88 to 487.72 μg/ml. Except for sdhA and sdhD, the amino acid substitutions of P225F, P225L, N230I, H272Y, and H272R in the sdhB subunit from 24 (4 sensitive [S] and 20 resistant [R]), 5 (1 S and 4 R), 1 (S), 1 (R), and 8 (4 S and 4 R) strains, respectively, and the concurrent amino acid substitutions of G85A + I93V + M158V + V168I in the sdhC subunit from 5 (4 S and 1 R) strains were identified. A G143A substitution in cytochrome b was identified in 96 isolates that were resistant to pyraclostrobin and three that were sensitive to it. The Bcbi-143/144 intron was identified in the other three isolates sensitive to pyraclostrobin, but it was absent in the isolates that harbored the G143A mutation. The results showed that the populations of B. cinerea on ginseng have developed strong resistance to pyraclostrobin. Therefore, it is not recommended to continue using this fungicide to control gray mold on P. ginseng. Boscalid is still effective against most isolates. However, to prevent fungicide resistance, it is recommended to use a mixture of boscalid with other categories of fungicides.

Target and non-target site mechanisms of fungicide resistance and their implications for the management of crop pathogens

Fungicides are indispensable for high-quality crops, but the rapid emergence and evolution of fungicide resistance have become the most important issues in modern agriculture. Hence, the sustainability and profitability of agricultural production have been challenged due to the limited number of fungicide chemical classes. Resistance to site-specific fungicides has principally been linked to target and non-target site mechanisms. These mechanisms change the structure or expression level, affecting fungicide efficacy and resulting in different and varying resistance levels. This review provides background information about fungicide resistance mechanisms and their implications for developing anti-resistance strategies in plant pathogens. Here, our purpose was to review changes at the target and non-target sites of quinone outside inhibitor (QoI) fungicides, methyl-benzimidazole carbamate (MBC) fungicides, demethylation inhibitor (DMI) fungicides, and succinate dehydrogenase inhibitor (SDHI) fungicides and to evaluate if they may also be associated with a fitness cost on crop pathogen populations. The current knowledge suggests that understanding fungicide resistance mechanisms can facilitate resistance monitoring and assist in developing anti-resistance strategies and new fungicide molecules to help solve this issue. © 2023 Society of Chemical Industry.

Succinate Dehydrogenase Subunit C Contributes to Mycelial Growth and Development, Stress Response, and Virulence in the Insect Parasitic Fungus Beauveria bassiana

Succinate dehydrogenase (SDH), also known as respiratory chain complex II, plays a crucial role in energy production in which SdhC functions as an anchored subunit in the inner membrane of mitochondria. In this study, domain annotation analyses revealed that two SdhC domain-containing proteins were present in the filamentous insect-pathogenic fungus Beauveria bassiana, and they were named BbSdhC1 and BbSdhC2, respectively. Only BbSdhC1 localized to mitochondria; hence, this protein is considered the ortholog of SdhC in B. bassiana. Ablation of BbSdhC1 led to significantly reduced vegetative growth on various nutrients. The ΔBbsdhc1 mutant displayed the significantly reduced ATP synthesis and abnormal differentiation under aerial and submerged conditions. Notably, the BbSdhC1 loss resulted in enhanced intracellular levels of reactive oxygen species (ROS) and impaired growth of mycelia under oxidative stress. Finally, insect bioassays (via cuticle and intrahemocoel injection infection) revealed that disruption of BbSdhC1 significantly attenuated fungal virulence against the insect hosts. These findings indicate that BbSdhC1 contributes to vegetative growth, resistance to oxidative stress, differentiation, and virulence of B. bassiana due to its roles in energy generation and maintaining the homeostasis of the intracellular ROS levels. IMPORTANCE The electron transport chain (ETC) is critical for energy supply by mediating the electron flow along the mitochondrial membrane. Succinate dehydrogenase (SDH) is also known as complex II in the ETC, in which SdhC is a subunit anchored in mitochondrial membrane. However, the physiological roles of SdhC remain enigmatic in filamentous fungi. In filamentous insect-pathogenic fungus B. bassiana, SdhC is required for maintaining mitochondrial functionality, which is critical for fungal stress response, development, and pathogenicity. These findings improve our understanding of physiological mechanisms of ETC components involved in pathogenicity of the entomopathogenic fungi.

SdhC-I86F Mutation in Phakopsora pachyrhizi Is Stable and Can Be Related to Fitness Penalties

Succinate dehydrogenase inhibitors (SDHIs) fungicides are used to control Asian soybean rust (Phakopsora pachyrhizi), and the SdhC-I86F mutation is related to pathogen resistance. The objective of this study was to determine whether fitness penalties are associated with SDHI resistance (SdhC-I86F mutation) in P. pachyrhizi populations. Moreover, the study investigated whether the SdhC-I86F mutation remained stable after the fungus propagation both in the absence and presence of fungicide. The populations used in this study presented mutations for all genes analyzed (Cyp51, Cytb, and SdhC), except for a wild-type population (WT_SdhC) found with no SdhC-I86F mutation. The frequencies of the SdhC-I86F mutant populations were stable after 36 generations in the absence of fungicide. However, in the case of the WT_SdhC population, the SdhC-I86F mutation was further detected after one generation of the fungus in the presence of the SDHI fungicide, according to the results of a detached leaf assay. Three tests were performed to evaluate fitness components and sensitivity to fungicides (half maximal effective concentration). SdhC-I86F mutant populations were more sensitive to osmotic and oxidative stress than the WT_SdhC population; however, the sensitivity to ultraviolet radiation was similar for both populations. All mutated populations were less sensitive than the WT_SdhC when using SDHI (azoxystrobin + benzovindiflupyr), but more sensitive to mancozeb. The presence of fitness penalties, the mutation stability, and the sensitivity to mancozeb presented by the SdhC-I86F mutant populations can be relevant to the management of the disease in the field.

Crystallographic investigation of the ubiquinone binding site of respiratory Complex II and its inhibitors

The quinone binding site (Q-site) of Mitochondrial Complex II (succinate-ubiquinone oxidoreductase) is the target for a number of inhibitors useful for elucidating the mechanism of the enzyme. Some of these have been developed as fungicides or pesticides, and species-specific Q-site inhibitors may be useful against human pathogens. We report structures of chicken Complex II with six different Q-site inhibitors bound, at resolutions 2.0-2.4 Å. These structures show the common interactions between the inhibitors and their binding site. In every case a carbonyl or hydroxyl oxygen of the inhibitor is H-bonded to Tyr58 in subunit SdhD and Trp173 in subunit SdhB. Two of the inhibitors H-bond Ser39 in subunit SdhC directly, while two others do so via a water molecule. There is a distinct cavity that accepts the 2-substituent of the carboxylate ring in flutolanil and related inhibitors. A hydrophobic "tail pocket" opens to receive a side-chain of intermediate-length inhibitors. Shorter inhibitors fit entirely within the main binding cleft, while the long hydrophobic side chains of ferulenol and atpenin A5 protrude out of the cleft into the bulk lipid region, as presumably does that of ubiquinone. Comparison of mitochondrial and Escherichia coli Complex II shows a rotation of the membrane-anchor subunits by 7° relative to the iron‑sulfur protein. This rotation alters the geometry of the Q-site and the H-bonding pattern of SdhB:His216 and SdhD:Asp57. This conformational difference, rather than any active-site mutation, may be responsible for the different inhibitor sensitivity of the bacterial enzyme.

A Method for the Examination of SDHI Fungicide Resistance Mechanisms in Phytopathogenic Fungi Using a Heterologous Expression System in Sclerotinia sclerotiorum

Succinate dehydrogenase inhibitors (SDHIs) are a class of broad-spectrum fungicides used for management of diseases caused by phytopathogenic fungi. In many cases, reduced sensitivity to SDHI fungicides has been correlated with point mutations in the SdhB and SdhC target genes that encode components of the succinate dehydrogenase complex. However, the genetic basis of SDHI fungicide resistance mechanisms has been functionally characterized in very few fungi. Sclerotinia sclerotiorum is a fast-growing and SDHI fungicide-sensitive phytopathogenic fungus that can be conveniently transformed. Given the high amino acid sequence similarity and putative structural similarity of SDHI protein target sites between S. sclerotiorum and other common phytopathogenic ascomycete fungi, we developed an in vitro heterologous expression system that used S. sclerotiorum as a reporter strain. With this system, we were able to demonstrate the function of mutant SdhB or SdhC alleles from several ascomycete fungi in conferring resistance to multiple SDHI fungicides. In total, we successfully validated the function of Sdh alleles that had been previously identified in field isolates of Botrytis cinerea, Blumeriella jaapii, and Clarireedia jacksonii (formerly S. homoeocarpa) in conferring resistance to boscalid, fluopyram, or fluxapyroxad and used site-directed mutagenesis to construct and phenotype a mutant allele that is not yet known to exist in Monilinia fructicola populations. We also examined the functions of these alleles in conferring cross-resistance to more recently introduced SDHIs including inpyrfluxam, pydiflumetofen, and pyraziflumid. The approach developed in this study can be widely applied to interrogate SDHI fungicide resistance mechanisms in other phytopathogenic ascomycetes.

Development of Boscalid Resistance in Botrytis cinerea and an Efficient Strategy for Resistance Management

Among succinate dehydrogenase inhibitors, only boscalid has been registered in China for controlling gray mold. In Shandong Province of China, it has been more than a decade since the first use of boscalid to control gray mold. In the current study, we monitored the resistance development process of Botrytis cinerea to boscalid, identified the mutation types that occurred in boscalid-resistant isolates, and proposed an original application technique to delay resistance development. A total of 720 B. cinerea isolates collected from tomato and cucumber in Shandong Province from 2014 to 2019 were determined to be sensitive to boscalid. The results showed that the sensitivity of the B. cinerea isolates to boscalid declined gradually over time, with a mean half maximal effective concentration of 0.3 ± 0.02 mg/liter in 2014 and 6.39 ± 1.66 mg/liter in 2019. The proportion of resistant isolates quickly increased from 0.81% in 2014 to 28.97% in 2019. Mutations of P225F, N230I, H272Y, and H272R in the SdhB subunit were responsible for boscalid resistance. Four concurrent mutations (G85A, I93V, M158V, and V168I) in the SdhC subunit were first discovered in Shandong Province, but they did not affect the level of boscalid resistance. Interestingly, this study found that the fruit dipping application, a precise topical application technique, could delay the development of boscalid resistance. Therefore, this application technique provides a new method for resistance management of B. cinerea.

Resistance to Boscalid in Botrytis cinerea From Greenhouse-Grown Tomato

Gray mold, caused by the fungus Botrytis cinerea Pers ex Fr., is one of the most destructive spoilage diseases, severely affecting tomato production in Henan Province, China. Spraying fungicides from the flowering to the harvest stage is a necessary measure to reduce losses associated with B. cinerea infection. However, B. cinerea has developed resistance to fungicides in many countries. Boscalid is a succinate dehydrogenase inhibitor (SDHI) fungicide and was registered for the control of gray mold. In this study, a total of 269 B. cinerea isolates were collected from tomato in commercial greenhouses in different locations of Henan Province in 2014 and 2015. The sensitivity and resistance of B. cinerea field isolates were determined based on mycelial growth. The effective concentration 50 ranged from 0.11 to 15.92 µg/ml and 0.16 to 8.54 µg/ml, in 2014 and 2015, respectively. The frequency of low resistance to boscalid was 12.6 and 7.6%, and moderate resistance was 2.7 and 1.3% in 2014 and 2015, respectively. No highly resistant isolates were found in Henan Province, China. Mycelial growth, mycelial dry weight, spore production, and pathogenicity were not significantly different between resistant and sensitive phenotypes of the B. cinerea isolates. The results of cross-resistance testing showed no correlation between boscalid and carbendazim, procymidone, pyrimethanil, fluazinam, or fluopyram. In this study, the succinate dehydrogenase genes B (sdhB), C (sdhC), and D (sdhD) were analyzed and compared in sensitive and low-resistance and moderately resistant B. cinerea isolates to boscalid. Results showed that point mutations occurred simultaneously at sdhC amino acid positions 85 (G85A), 93 (I93V), 158 (M158V), and 168 (V168I) in 4 out of 10 sensitive isolates and 23 of 26 low-resistance and 5 of 5 moderately resistant B. cinerea isolates to boscalid. No point mutations were found in the sdhB and sdhD genes of all isolates. Furthermore, no point mutations were found in sdhB, sdhC, and sdhD genes in 3 of 26 low-resistance B. cinerea isolates to boscalid. Therefore, we speculate that the simultaneous point mutations in the sdhC gene may not be related to the resistance of B. cinerea to boscalid. These results suggested that there might be a substitution mechanism for the resistance of B. cinerea to the SDHI fungicide boscalid.