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Characterization of bacterial degradation systems for cyclodiene and strobirulin pesticides

ALIAS, AMIRAH 東京大学 DOI:10.15083/0002004916

2022.06.22

概要

Chapter 1: Introduction
Chlorinated cyclodiene such as 6,7,8,9,10,10-hexachloro-1,5,5a,6,9,9a-hexahydro-6,9-methano-2,4,3- benzodioxathiepine-3-oxide or endosulfan had been commonly used on crops and cotton fields before being banned worldwide due to high toxicity in living organisms. Despite being phased out globally, unrestricted usage of endosulfan at agricultural sites remains, as traces of endosulfan may still be found in the soil. Nevertheless, endosulfan can undergo microbial-assisted degradation by two possible routes: oxidation of the parent compound to yield more toxic metabolite, endosulfan sulfate, or hydrolyzed into polar metabolites such as endosulfan diol. Various bacteria that can degrade endosulfan have been isolated and several degradation pathways have been studied so far. However, characterization of genes required for the endosulfan transformation is severely insufficient. The only characterized endosulfan monooxygenases, Esd and Ese, isolated from Mycobacterium sp. ESD and Anthrobacter sp. KW, respectively, are involved in converting endosulfan into either endosulfan monoaldehyde and endosulfan hydroxyether (by Mycobacterium sp. ESD) or to endosulfan monoalcohol (by Anthrobacter sp. KW). Both the genes, however, express only during sulfur starvation.

Meanwhile, synthetic strobilurins such as azoxystrobin (hereafter AZ), kresoxim methyl (hereafter KRM) and trifloxystrobin (hereafter TRF) possess key component of toxophore, called β-methoxyacrylate or chemically similar methoxyiminoacetate, to act as active compound against numerous fungal plant pathogens by blocking the Q0 site of Complex III during mitochondrial respiration. Bacillus licheniformis strain TAB7 was first isolated from composting livestock waste in Japan and subsequently patented by Toyota Motor Corp as compost deodorant under the commercial name ResQ. Apart from deodorizing properties, TAB7 also has the ability to promote plant growth by synthesizing indole-3-acetic acid (IAA) by tryptophan-dependent pathway via either IAM, IAN, IPyA, or TAM pathway (Mpofu et al., 2019, Microbiol Resour Announc 8: 4 e01659-18). Besides, during early screening of agrochemicals transformation, TAB7 can degrade 80% of AZ (100 ppm), 87% of KRM (100 ppm) and 97% of TRF (100 ppm) after 30, 10 and 10 days of incubation, respectively (Mpofu, Doctoral thesis 2019), during resting cell assays in rich L-broth (LB) medium. Major transformation products of strobilurins reported so far are carboxylic acid derivative via hydrolysis of the methyl ester group by subtilisin-like proteases. Biotransformation of AZ by TAB7, however, produced two metabolites, one of which has been confirmed to be (E)-AZ amine by 13C-NMR, and NOESY analysis. The structural confirmation of AZ metabolite has provided evidence that TAB7 may have a novel azoxystrobin degradation pathway as such metabolite has not been reported in bacteria so far. アミラ アリアス Thus, this evidence serves as the basis to study the previously uncharacterized enzymes responsible for AZ degradation pathway in TAB7. On the other hand, degradation product(s) of KRM and TRF by TAB7 has not been determined so far, thus also becoming one of the interests in this study

Chapter 2: Isolation of endosulfan degrader and screening for endosulfan-metabolizing enzymes
A total of 71 soil samples from Thailand, Japan, and Malaysia were collected from September 2016 until June 2017. Based on the initial screening, 8 isolates (Table 1) and Rhodococcus jostii RHA1, a known PCB-degrader (McLeod et al, 2006, Proc Natl Acad Sci USA. 103:15582-15587), were selected to assess for endosulfandegrading ability in carbon-free (CFM) or sulfur-free (SFM) medium, supplemented with endosulfan (20 ppm). 16S rRNA phylogeny showed that the isolates belong to either metabolically diverse β-proteobacteria or actinobacteria, similar with Mycobacterium sp. ESD and Anthrobacter sp. KW.

Based on HPLC analysis, strains S9 and S12 showed the highest ability to degrade endosulfan after 20 days of incubation (Fig. 1), especially in SFM. Both strains were isolated from soil that had history of endosulfan application as traces of endosulfan were detected in the soil from the same location. LC-MS/MS analysis during Multiple Reaction Monitoring (MRM) scanning in negative ion mode confirmed that the metabolite produced by strain S9 and strain S12 is a diol, based on fragmentation pattern of daughter ions (m/z 284.913 and m/z 212.887) which are identical with those of endosulfan diol standard (MW 356.827), suggesting that different set of enzyme(s) are responsible for the transformation (Fig. 2).

In order to identify the enzymes, whole genome sequencing of strains S9, S12, M1257 and M1651 was performed using Illumina platform and post-sequencing analysis was performed using CLC Genomics Workbench. The data was assembled through de novo assembly by CLC, resulting in 1805, 1847, 67, 371 contigs for S9, S12, M1257, and M1651, respectively with average depth of 150X, 154X, 159X, 149X, respectively. Several ORFs encoding Fe-dependent sulfatases as well as Esd and Ese homologs have been identified. Local BLAST search using homologous amino acid sequences of known sulfatases (EC 3.1.6) in draft genome of S9 and S12 enabled identification of putative sulfatases (83-97% coverage, 39-51% identity) and Ese/Esd homologs (84-98% coverage, 24-36% identity) in S9, however, low homology at amino acid level was found for both sulfatases and Ese/Esd homologs in S12.

Chapter 3: Biotransformation of strobilurin fungicides by B. licheniformis TAB 7
To check reproducibility of previous data, time-course assays were performed using TAB7 grown in LB medium supplemented with either one of the strobilurins (100 ppm). The results showed that TAB7 completely mineralized KRM within 9 days whereas 60% TRF and AZ were degraded after 9 and 30 days of incubation, respectively (Fig 3: A-C).

Similarly, TAB7 could degrade AZ into two metabolite peaks, one of which was previously identified to be (E)-AZ-amine while metabolite peak B contains a mixture of (Z)-AZ and (Z)-AZ amine at 2:5 ratio. This ratio, however, is dependent on purification steps prior to NMR analysis. Isomerization of (E)-AZ is unlikely to be due to abiotic photolysis but a product of TAB7 metabolism. Therefore, AZ transformation pathway by TAB7 was proposed (Fig 4) as the methoxy group is replaced by hydroxyl group by enol-keto tautomerization (reaction 1) before transamination (reaction 2) to replace C=O with an amine. Reaction 1 and 2 are hypothesized to be catalyzed by O-demethylases and transaminases, respectively. Genome wide search for putative enzymes in TAB7 genome (GenBank ID: CP027789) was performed, revealing 6 putative genes for cytochrome P450 and 3 FAD-depended amine oxidases for reaction 1 and 8 transaminase genes for reaction 2. TRF, on the other hand, was transformed into two new metabolites, both of which were collected and purified in order to identify the products using LC-MS/MS. The identity of TRF metabolite was confirmed to be TRF acid, in accordance to reported literature (Chen et al., 2008, Agric. Food Chem., 56, 1829–1837, Clinton et al. 2011, Biocatal Biotransfor, 29:4, 119-129). In the case of KRM, no metabolite peak was detected during time course assay.

To investigate bioactivity of (E)-AZ amine against rice blast fungus and compare the activity of the metabolite against the parent compound, TAB7 was incubated in the presence of AZ (100 ppm) for 30 days and (E)-AZ amine was purified by HPLC. 60% of NADH-cytochrome c oxidoreductase activity of Magnaporthe oryzae race 007.0 Ina86-137 was inhibited by (E)-AZ amine at 0.2 mM, as opposed to azoxystrobin at 0.098 mM, suggesting (E)- AZ amine had lower toxicity than the parent compound.

Chapter 4: Summary and future prospects
In this study, endosulfan-degrading potential between environmental isolates from multiple sources was assessed. Streptomyces sp. strains S9 and S12 were found to have highest degradation ability. Metabolites produced by S9 and S12 in both CFM and SFM were confirmed to be endosulfan diol by LC-MS/MS. BLAST search using homologous amino acid sequences of known sulfatases in draft genome of S9 and S12 identified putative sulfatases and Ese/Esd homologs in S9, however, low homology at amino acid level was found for both sulfatases and Ese/Esd homologs in S12. Cloning of gene candidates in S9 is currently in progress whereas RNA sequencing to identity responsible endosulfan hydrolyzing enzymes in S12 strain becomes the future prospect in Chapter 2. In Chapter 3, strobilurin degradation metabolites by TAB7 were identified. TAB7 transformed AZ into (Z)-AZ, (E)-AZ amine and (Z) AZ amine. (E)-AZ amine had lower activity than the parent compound, AZ. Meanwhile, TAB7 could transform TRF into TRF acid but degradation product of KRM could not be detected despite sharing similar methoxyiminoacetate toxophore. Structural information of these TRF and AZ metabolites are of great importance to elucidate the putative enzymes responsible for such transformation and strobilurins degradation pathway in TAB7. As prolonged incubation of AZ in LB for 60 days did not show any other metabolites, it is necessary to set up longer term incubation or growth culture utilizing TAB7 supplemented with either (Z)-AZ, (E)-AZ amine or (Z) AZ amine separately to provide more information on the behavior of TAB7 transforming the pesticide thus, becoming one of the future prospects for this chapter.

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