ABC transporters linked to multiple herbicide resistance in blackgrass (Alopecurus myosuroides)

Genome-Wide Dissection of Novel QTLs and Genes Associated with Weed Competitiveness in Early-Backcross Selective Introgression-Breeding Populations of Rice (Oryza sativa L.)

The direct-seeded rice (DSR) system is poised to become the dominant rice cultivation method due to its advantages, including reduced water usage, less labor requirements, decreased greenhouse gas emissions, and improved adaptation to climate change. However, weeds, particularly jungle rice (Echinochloa colona), significantly hinder DSR and cause substantial yield losses. This study aimed to develop rice cultivars competitive against jungle rice through selective breeding, focusing on early seed germination (ESG) and seedling vigor (ESV). We utilized 181 early-backcross selective introgression breeding lines (EB-SILs) developed using Green Super Rice (GSR) technology by backcrossing Weed Tolerant Rice1 (WTR1) with three donor parents, Haoannong, Cheng Hui 448, and Y134. Using the tunable genotyping-by-sequencing (tGBS®, Data2Bio Technologies, Ames, IA, USA) method, we identified 3971 common single nucleotide polymorphisms (SNPs) that facilitated the mapping of 19 novel quantitative trait loci (QTLs) associated with weed competitiveness-eight linked to ESG traits and eleven to ESV traits. Notably, all QTLs were novel except qRPH1, linked to relative plant height at 14 and 21 days after sowing. Key QTLs were located on chromosomes 2, 3, 5, 6, 8, 9, 10, and 12. Candidate genes identified within these QTLs are implicated in the plant's response to various abiotic and biotic stresses. Our findings enhance the understanding of the genetic basis for ESG and ESV traits critical for weed competitiveness, supporting marker-assisted and genomic selection approaches for breeding improved rice varieties. Furthermore, this research lays the groundwork for employing gene expression, cloning, and CRISPR editing strategies to combat jungle rice, with potential applications for other weed species and contributing to effective integrated weed management in the DSR system.

Identification of metabolic enzyme genes linked to mesosulfuron-methyl resistance in Bromus japonicus

Bromus japonicus is a very troublesome weed in major winter wheat fields in China and substantially reduces wheat yield. Resistance to acetolactate synthase (ALS)-inhibiting herbicides in B. japonicus has become increasingly prevalent in recent years. While the mechanism of target site resistance (TSR) to ALS-inhibiting herbicides in B. japonicus has been well elucidated, the understanding of non-target site resistance (NTSR) remains limited. In this study, we identified a B. japonicus population (BJ-NTSR-1) which has developed resistance to mesosulfuron-methyl. Compared to the mesosulfuron-methyl-susceptible population (BJ-S), the resistance level of BJ-NTSR-1 was found to be 22.56 times higher. Based on the results of ALS gene sequencing and relative expression analyses, TSR was not detected in the BJ-NTSR-1 population. Additionally, pretreatment with cytochrome P450 (CYP450) and glutathione S-transferase (GST) inhibitors did not reverse the resistance to mesosulfuron-methyl in BJ-NTSR-1 population. RNA-seq and RT-qPCR analyses revealed that, three uridine 5'-diphospho-glucosyl transferase (UGT) genes (UGT76F1, UGT88F5, and UGT85A1), four ATP-binding cassette (ABC) transporter genes (ABCB19s, ABCG1, and ABCB21), and three CYP450 genes (CYP71C1, CYP71C2, and CYP72A15) are significantly upregulated in the BJ-NTSR-1 population. Among these genes, the overexpression of ABCG1 enhanced yeast resistance to mesosulfuron-methyl. These genes are likely involved in mediating NTSR to mesosulfuron-methyl in the BJ-NTSR-1 population. This study presents the first global report that CYP450, UGT, and ABC transporter genes may collectively mediate NTSR to ALS-inhibiting herbicides in Brome species.

Overexpression of cytochrome P450 CYP71AF43 contributing resistance to fenoxaprop-P-ethyl in Alopecurus myosuroides from China

Black-grass (Alopecurus myosuroides), one of the most economically destructive herbicide-resistant weeds in Europe, is rapidly expanding in winter wheat regions of China. In recent years, the recommended application rate of fenoxaprop-P-ethyl in the field has failed to effectively control Alopecurus myosuroides populations, thereby threatening wheat yields at risk. In this study, we collected a suspected herbicide-resistant population (R-HB) of Alopecurus myosuroides from a wheat field in Hebei Province and confirmed its resistance to fenoxaprop-P-ethyl, with a resistance index of 26.73-fold. Sensitivity analyses of other ACCase-inhibiting herbicides revealed cross-resistance in the R-HB population to clethodim and pinoxaden. Molecular analysis indicated that the resistance phenotype in this population was not due to alterations in the target site. Pretreatment with the cytochrome P450 (P450) inhibitor malathion partially reversed fenoxaprop-P-ethyl resistance in the R-HB population. RNA-seq and RT-qPCR validation revealed the constitutive overexpression of the P450 gene CYP71AF43 in the R-HB population. Molecular docking predictions suggest that the CYP71AF43 protein may have metabolic activity toward fenoxaprop-P-ethyl. In genetically modified yeast, overexpression of AmCYP71AF43 was found to enhance tolerance to fenoxaprop-P-ethyl, but not to clethodim and pinoxaden. Additionally, rice calli overexpressing the AmCYP71AF43 gene exhibited resistance to fenoxaprop-P-ethyl, but not to clethodim or pinoxaden. Collectively, the increased expression of CYP71AF43 may enhance P450-mediated metabolism, conferring resistance to fenoxaprop-P-ethyl in the R-HB population. This is the first report of this mechanism in Alopecurus myosuroides. This discovery provides a novel perspective for the in-depth analysis of resistance mechanisms in weeds against the ACCase-inhibiting herbicide fenoxaprop-P-ethyl.

Functional Characterization of Cytochromes P450 Linked to Herbicide Detoxification and Selectivity in Winter Wheat and the Problem Competing Weed Blackgrass

The selective chemical control of wild grasses in wheat is primarily determined by the relative rates of herbicide metabolism, with the superfamily of cytochromes P450 (CYPs) playing a major role in catalyzing phase 1 detoxification reactions. This selectivity is enhanced by herbicide safeners, which induce CYP expression in cereals, or challenged by the evolution of nontarget site resistance (NTSR) in weeds such as blackgrass. Using transcriptomics, proteomics, and functional expression in recombinant yeast, CYPs linked to safener treatment and NTSR have been characterized in wheat and blackgrass. Safener treatment resulted in the induction of 13 families of CYPs in wheat and 5 in blackgrass, with CYP71, CYP72, CYP76, and CYP81 members active toward selective herbicides in the crop. Based on their expression and functional activities, three inducible TaCYP81s were shown to have major roles in safening in wheat. In contrast, a single AmCYP81 that was enhanced by NTSR, but not by safening, was found to dominate herbicide detoxification in blackgrass.

Characterization of a Topramezone-Resistant Rice Mutant TZR1: Insights into GST-Mediated Detoxification and Antioxidant Responses

Mutagenesis breeding, combined with the application of corresponding herbicides to develop herbicide-resistant rice germplasm, provides great promise for the management of weeds and weedy rice. In this study, a topramezone-resistant rice mutant, TZR1, was developed from the indica rice line Chuangyu 9H (CY9H) through radiation mutagenesis and topramezone selection. Dose-response curves revealed that the resistance index of TZR1 to topramezone was 1.94-fold compared to that of CY9H. The resistance mechanism of TZR1 was not due to target-site resistance. This resistance could be reversed by a specific inhibitor of glutathione S-transferase (GST). The activity of antioxidant enzymes was analyzed. SNPs and Indels were detected using whole-genome resequencing; differentially expressed genes were identified through RNA sequencing. Then, they underwent Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses. Key candidate genes associated with topramezone resistance were validated via a real-time quantitative PCR assay. Five GST genes, two UDP-glycosyltransferase genes, and three ATP-binding cassette transporter genes were identified as potential contributors to topramezone detoxification in TZR1. Overall, these findings suggest that GST enzymes possibly play an important role in TZR1 resistance to topramezone. This study will provide valuable information for the scientific application of 4-hydroxyphenylpyruvate dioxygenase inhibitors in paddy fields in future.

Amelioration of arsenic-induced hepatic injury via sulfated glycosaminoglycan from swim bladder: Modulation of Nrf2 pathway and amino acid metabolism

Arsenic, a known environmental pollutant with a carcinogenic risk, is associated with chronic liver toxicity. Prebiotic regulation represents an emerging dietary strategy to alleviate arsenic-induced hepatotoxicity; however, research in this area remains limited. This study employed sulfated swim bladder glycosaminoglycan (SBSG), a potential prebiotic, to assess its efficacy in mitigating arsenic-induced liver injury. In basic indicators, SBSG resisted oxidative stress by down-regulating AST, ALT, MDA, and MPO, up-regulating antioxidants (T-SOD, GSH, and GSH-px), and ameliorating histopathological damage. RT-qPCR analysis revealed that SBSG could regulate the Nrf2 signaling pathway and affect the expression of o genes related to ferroptosis and detoxification. The expression of protein further verified that SBSG could play an antioxidant and detoxifying role as an Nrf2 activator. Non-targeted metabolomics results demonstrated that SBSG primarily addresses metabolic disorders by up-regulating D-amino acid metabolism, ABC transporter, and alanine, aspartate and glutamate metabolism. Correlation analysis suggests that SBSG alleviates arsenic-induced liver oxidative damage through mechanisms linked to the Nrf2 pathway and amino acid metabolism. This study provided a research basis for expanding the dietary strategy to reduce arsenic induced toxicity.

Pyroxsulam Resistance in Apera spica-venti: An Emerging Challenge in Crop Protection

Apera spica-venti, a prevalent weed in Czech winter wheat fields, has developed resistance to ALS-inhibiting herbicides due to their frequent use. This study reports a biotype of A. spica-venti resistant to pyroxsulam, with cross and multiple resistance to iodosulfuron, propoxycarbazone, pinoxaden, and chlortoluron. Dose-response experiments revealed high resistance of both R1 and R2 biotypes to pyroxsulam, with resistance factors (RF) of 6.69 and 141.65, respectively. Pre-treatment with malathion reduced RF by 2.40× and 1.25× in R1 and R2, indicating the potential involvement of cytochrome P450 (CytP450). NBD-Cl pre-treatment decreased RF only in R2, suggesting possible GST involvement. Gene analysis revealed no mutations (at previously reported sites) or overexpression in the acetolactate synthase (ALS) gene. However, a significant difference in ALS enzyme activity between resistant and susceptible biotypes points to target-site resistance mechanisms. Studies with 14C-labeled pyroxsulam showed that reduced absorption and translocation were not likely resistance mechanisms. In summary, herbicide resistance in A. spica-venti appears to result from multiple mechanisms. Possible causes include target-site resistance from an unidentified ALS mutation (within coding or regulatory regions). Enhanced herbicide metabolism via CytP450s and GSTs is also a contributing factor. Further experimental validation is needed to confirm these mechanisms and fully understand the resistance. This evolution underscores the adaptive capacity of weed populations under herbicide pressure, emphasizing the need for alternative control strategies.

Cellular and molecular aspects of drug resistance in cancers

OBJECTIVES

Cancer drug resistance is a multifaceted phenomenon. The present review article aims to comprehensively analyze the cellular and molecular aspects of drug resistance in cancer and the strategies employed to overcome it.

EVIDENCE ACQUISITION

A systematic search of relevant literature was conducted using electronic databases such as PubMed, Scopus, and Web of Science using appropriate key words. Original research articles and secondary literature were taken into consideration in reviewing the development in the field.

RESULTS AND CONCLUSIONS

Cancer drug resistance is a pervasive challenge that causes many treatments to fail therapeutically. Despite notable advances in cancer treatment, resistance to traditional chemotherapeutic agents and novel targeted medications remains a formidable hurdle in cancer therapy leading to cancer relapse and mortality. Indeed, a majority of patients with metastatic cancer experience are compromised on treatment efficacy because of drug resistance. The multifaceted nature of drug resistance encompasses various factors, such as tumor heterogeneity, growth kinetics, immune system, microenvironment, physical barriers, and the emergence of undruggable cancer drivers. Additionally, alterations in drug influx/efflux transporters, DNA repair mechanisms, and apoptotic pathways further contribute to resistance, which may manifest as either innate or acquired traits, occurring prior to or following therapeutic intervention. Several strategies such as combination therapy, targeted therapy, development of P-gp inhibitors, PROTACs and epigenetic modulators are developed to overcome cancer drug resistance. The management of drug resistance is compounded by the patient and tumor heterogeneity coupled with cancer's ability to evade treatment. Gaining further insight into the mechanisms underlying medication resistance is imperative for the development of effective therapeutic interventions and improved patient outcomes.

Comparative Characterization of Three Homologous Glutathione Transferases from the Weed Lolium perenne

The comparative analysis of homologous enzymes is a valuable approach for elucidating enzymes' structure-function relationships. Glutathione transferases (GSTs, EC. 2.5.1.18) are crucial enzymes in maintaining the homeostatic stability of plant cells by performing various metabolic, regulatory, and detoxifying functions. They are promiscuous enzymes that catalyze a broad range of reactions that involve the nucleophilic attack of the activated thiolate of glutathione (GSH) to electrophilic compounds. In the present work, three highly homologous (96-98%) GSTs from ryegrass Lolium perenne (LpGSTs) were identified by in silico homology searches and their full-length cDNAs were isolated, cloned, and expressed in E. coli cells. The recombinant enzymes were purified by affinity chromatography and their substrate specificity and kinetic parameters were determined. LpGSTs belong to the tau class of the GST superfamily, and despite their high sequence homology, their substrate specificity displays remarkable differences. High catalytic activity was determined towards hydroxyperoxides and alkenals, suggesting a detoxification role towards oxidative stress metabolites. The prediction of the structure of the most active LpGST by molecular modeling allowed the identification of a non-conserved residue (Phe215) with key structural and functional roles. Site-saturation mutagenesis at position 215 and the characterization of eight mutant enzymes revealed that this site plays pleiotropic roles, affecting the affinity of the enzyme for the substrates, catalytic constant, and structural stability. The results of the work have improved our understanding of the GST family in L. perenne, a significant threat to agriculture, sustainable food production, and safety worldwide.

Haplotypes of ATP-Binding Cassette CaABCC6 in Chickpea from Kazakhstan Are Associated with Salinity Tolerance and Leaf Necrosis via Oxidative Stress

Salinity tolerance was studied in chickpea accessions from a germplasm collection and in cultivars from Kazakhstan. After NaCl treatment, significant differences were found between genotypes, which could be arranged into three groups. Those that performed poorest were found in group 1, comprising five ICC accessions with the lowest chlorophyll content, the highest leaf necrosis (LN), Na+ accumulation, malondialdehyde (MDA) content, and a low glutathione ratio GSH/GSSG. Two cultivars, Privo-1 and Tassay, representing group 2, were moderate in these traits, while the best performance was for group 3, containing two other cultivars, Krasnokutsky-123 and Looch, which were found to have mostly green plants and an exact opposite pattern of traits. Marker-trait association (MTA) between 6K DArT markers and four traits (LN, Na+, MDA, and GSH/GSSG) revealed the presence of four possible candidate genes in the chickpea genome that may be associated with the three groups. One gene, ATP-binding cassette, CaABCC6, was selected, and three haplotypes, A, D1, and D2, were identified in plants from the three groups. Two of the most salt-tolerant cultivars from group 3 were found to have haplotype D2 with a novel identified SNP. RT-qPCR analysis confirmed that this gene was strongly expressed after NaCl treatment in the parental- and breeding-line plants of haplotype D2. Mass spectrometry of seed proteins showed a higher accumulation of glutathione reductase and S-transferase, but not peroxidase, in the D2 haplotype. In conclusion, the CaABCC6 gene was hypothesized to be associated with a better response to oxidative stress via glutathione metabolism, while other candidate genes are likely involved in the control of chlorophyll content and Na+ accumulation.

Genome-wide study of glutathione transferases and their regulation in flufenacet susceptible and resistant black-grass (Alopecurus myosuroides Huds.)

BACKGROUND

Glutathione transferases (GSTs) are enzymes with a wide range of functions, including herbicide detoxification. Up-regulation of GSTs and their detoxification activity enables the grass weed black-grass (Alopecurus myosuroides Huds.) to metabolize the very-long-chain fatty acid synthesis inhibitor flufenacet and other herbicides leading to multiple herbicide resistance. However, the genomic organization and regulation of GSTs genes is still poorly understood.

RESULTS

In this genome-wide study the location and expression of 115 GSTs were investigated using a recently published black-grass genome. Particularly, the most abundant GSTs of class tau and phi were typically clustered and often followed similar expression patterns but possessed divergent upstream regulatory regions. Similarities were found in the promoters of the most up-regulated GSTs, which are located next to each other in a cluster. The binding motif of the E2F/DP transcription factor complex in the promoter of an up-regulated GST was identical in susceptible and resistant plants, however, adjacent sequences differed. This led to a stronger binding of proteins to the motif of the susceptible plant, indicating repressor activity.

CONCLUSIONS

This study constitutes the first analysis dealing with the genomic investigation of GST genes found in black-grass and their transcriptional regulation. It highlights the complexity of the evolution of GSTs in black-grass, their duplication and divergence over time. The large number of GSTs allows weeds to detoxify a broad spectrum of herbicides. Ultimately, more research is needed to fully elucidate the regulatory mechanisms of GST expression. © 2024 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

The Cys-2088-Arg mutation in the ACCase gene and enhanced metabolism confer cyhalofop-butyl resistance in Chinese sprangletop (Leptochloa chinensis)

Acetyl-CoA carboxylase (ACCase)-inhibiting herbicides are among the most commonly used herbicides to control grassy weeds, especially Leptochloa chinensis, in rice fields across China. Herein, we collected a suspected resistant (R) population of L. chinensis (HFLJ16) from Lujiang county in Anhui Province. Whole plant dose response tests showed that, compared with the susceptible (S) population, the R population showed high resistance to cyhalofop-butyl (22-fold) and displayed cross-resistance to metamifop (9.7-fold), fenoxaprop-P-ethyl (18.7-fold), quizalofop-P-ethyl (7.6-fold), clodinafop-propargyl (12-fold) and clethodim (8.4-fold). We detected an amino acid substitution (Cys-2088-Arg) in the ACCase of resistant L. chinensis. However, ACCase gene expression levels were not significantly different (P > 0.05) between R plants and S plants, without or with cyhalofop-butyl treatment. Furthermore, pretreatment with piperonyl butoxide (PBO, a cytochrome P450 monooxygenase (CYP450) inhibitor) or 4-chloro-7-nitrobenzoxadiazole (NBD-Cl, a glutathione-S-transferase (GST) inhibitor), inhibited the resistance of the R population to cyhalofop-butyl significantly (by approximately 60% and 26%, respectively). Liquid chromatography tandem mass spectrometry analysis showed that R plants metabolized cyhalofop-butyl and cyhalofop acid (its metabolite) significantly faster than S plants. Three CYP450 genes, one GST gene, and two ABC transporter genes were induced by cyhalofop-butyl and were overexpressed in the R population. Overall, GST-associated detoxification, CYP450 enhancement, and target-site gene mutation are responsible for the resistance of L. chinensis to cyhalofop-butyl.

Comprehensive insights into herbicide resistance mechanisms in weeds: a synergistic integration of transcriptomic and metabolomic analyses

Omics techniques, including genomics, transcriptomics, proteomics, and metabolomics have smoothed the researcher's ability to generate hypotheses and discover various agronomically relevant functions and mechanisms, as well as their implications and associations. With a significant increase in the number of cases with resistance to multiple herbicide modes of action, studies on herbicide resistance are currently one of the predominant areas of research within the field of weed science. High-throughput technologies have already started revolutionizing the current molecular weed biology studies. The evolution of herbicide resistance in weeds (particularly via non-target site resistance mechanism) is a perfect example of a complex, multi-pathway integration-induced response. To date, functional genomics, including transcriptomic and metabolomic studies have been used separately in herbicide resistance research, however there is a substantial lack of integrated approach. Hence, despite the ability of omics technologies to provide significant insights into the molecular functioning of weeds, using a single omics can sometimes be misleading. This mini-review will aim to discuss the current progress of transcriptome-based and metabolome-based approaches in herbicide resistance research, along with their systematic integration.

Multiple herbicide resistance in a Cyperus difformis population in rice field from China

Herbicide resistance is rapidly emerging in Cyperus difformis in rice fields across China. The response of a C. difformis population GX-35 was tested against five acetolactate synthase (ALS)-inhibiting herbicides, auxin herbicide MCPA and photosynthesis II (PSII)-inhibitor bentazone. Population GX-35 evolved multiple resistance to ALS-inhibiting herbicides (penoxsulam, bispyribac‑sodium, pyrazosulfuron-ethyl, halosulfuron-methly and imazapic) and auxin herbicide MCPA, with resistance levels of 140-, 1253-, 578-, 18-, 13-, and 21-fold, respectively, compared to the susceptible population. In this population, ALS gene expression was similar to that of the susceptible population. However, an Asp376Glu mutation in ALS gene was observed, leading to reduced inhibition of in-vitro ALS activities by five ALS-inhibiting herbicides. Furthermore, CYP71D8, CYP77A3, CYP78A5 and three ABC transporter genes (cluster-14412.23067, cluster-14412.25321, and cluster-14412.24716) over-expressed in absence of penoxsulam. On the other hand, an UGT73C1 and an ABC transporter (cluster-14412.25038) were induced by penoxsulam. Additionally, both over-expression and induction were observed for CYP74, CYP71A1, UGT88A1 and an ABC transporter (cluster-14412.21723). The GX-35 population has indeed evolved multiple herbicide resistance in China. Therefore, a diverse range of weed control tactics should be implemented in rice field.