1887

Graphical Abstract

Graphical Abstract

Biochemical and molecular analyses to reveal the regulation of catabolic pathways in the complete degradation of dioctyl phthalate isomers in sp.

Abstract

Bacterial strain GONU, belonging to the genus , was isolated from a municipal waste-contaminated soil sample and was capable of utilizing an array of endocrine-disrupting phthalate diesters, including di--octyl phthalate (DnOP) and its isomer di(2-ethylhexyl) phthalate (DEHP), as the sole carbon and energy sources. The biochemical pathways of the degradation of DnOP and DEHP were evaluated in strain GONU by using a combination of various chromatographic, spectrometric and enzymatic analyses. Further, the upregulation of three different esterases (, and ), a phthalic acid (PA)-metabolizing operon and a protocatechuic acid (PCA)-metabolizing operon were revealed based on whole genome sequence information and substrate-induced protein profiling by LC-ESI-MS/MS analysis followed by differential gene expression by real-time PCR. Subsequently, functional characterization of the differentially upregulated esterases on the inducible hydrolytic metabolism of DnOP and DEHP revealed that EstG5 is involved in the hydrolysis of DnOP to PA, whereas EstG2 and EstG3 are involved in the metabolism of DEHP to PA. Finally, gene knockout experiments further validated the role of EstG2 and EstG5, and the present study deciphered the inducible regulation of the specific genes and operons in the assimilation of DOP isomers.

Funding
This study was supported by the:
  • Bose Institute
    • Principle Award Recipient: NotApplicable
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License. The Microbiology Society waived the open access fees for this article.
Loading

Article metrics loading...

/content/journal/micro/10.1099/mic.0.001353
2023-06-29
2024-12-14
Loading full text...

Full text loading...

/deliver/fulltext/micro/169/6/mic001353.html?itemId=/content/journal/micro/10.1099/mic.0.001353&mimeType=html&fmt=ahah

References

  1. Zhang J, Zhang C, Zhu Y, Li J, Li X. Biodegradation of seven phthalate esters by Bacillus mojavensis B1811. Int Biodeterior Biodegrad 2018; 132:200–207 [View Article]
    [Google Scholar]
  2. Nahurira R, Ren L, Song J, Jia Y, Wang J et al. Degradation of Di(2-Ethylhexyl) Phthalate by a Novel Gordonia alkanivorans Strain YC-RL2. Curr Microbiol 2017; 74:309–319 [View Article] [PubMed]
    [Google Scholar]
  3. Ren L, Lin Z, Liu H, Hu H. Bacteria-mediated phthalic acid esters degradation and related molecular mechanisms. Appl Microbiol Biotechnol 2018; 102:1085–1096 [View Article] [PubMed]
    [Google Scholar]
  4. Philip JM, Aravind UK, Aravindakumar CT. Emerging contaminants in Indian environmental matrices - a review. Chemosphere 2018; 190:307–326 [View Article] [PubMed]
    [Google Scholar]
  5. Zhao H-M, Du H, Huang C-Q, Li S, Zeng X-H et al. Bioaugmentation of exogenous strain Rhodococcus sp. 2G can efficiently mitigate di(2-ethylhexyl) phthalate contamination to vegetable cultivation. J Agric Food Chem 2019; 67:6940–6949 [View Article] [PubMed]
    [Google Scholar]
  6. Zhang H, Lin Z, Liu B, Wang G, Weng L et al. Bioremediation of di-(2-ethylhexyl) phthalate contaminated red soil by Gordonia terrae RL-JC02: characterization, metabolic pathway and kinetics. Sci Total Environ 2020; 733:139138 [View Article] [PubMed]
    [Google Scholar]
  7. Li F, Liu Y, Wang D, Zhang C, Yang Z et al. Biodegradation of di-(2-ethylhexyl) phthalate by a halotolerant consortium LF. PLoS ONE 2018; 13:e0204324 [View Article] [PubMed]
    [Google Scholar]
  8. Wu X, Liang R, Dai Q, Jin D, Wang Y et al. Complete degradation of di-N-octyl phthalate by biochemical cooperation between Gordonia SP. strain JDC-2 and Arthrobacter SP. strain JDC-32 isolated from activated sludge. J Hazard Mater 2010; 176:262–268 [View Article] [PubMed]
    [Google Scholar]
  9. Singh N, Dalal V, Mahto JK, Kumar P. Biodegradation of phthalic acid esters (PAEs) and in silico structural characterization of mono-2-ethylhexyl phthalate (MEHP) hydrolase on the basis of close structural homolog. J Hazard Mater 2017; 338:11–22 [View Article] [PubMed]
    [Google Scholar]
  10. Wang Y, Yin B, Hong Y, Yan Y, Gu JD. Degradation of dimethyl carboxylic phthalate ester by Burkholderia cepacia DA2 isolated from marine sediment of South China Sea. Ecotoxicology 2008; 17:845–852 [View Article] [PubMed]
    [Google Scholar]
  11. Li J, Gu J-D. Complete degradation of dimethyl isophthalate requires the biochemical cooperation between Klebsiella oxytoca Sc and Methylobacterium mesophilicum Sr Isolated from Wetland sediment. Sci Total Environ 2007; 380:181–187 [View Article] [PubMed]
    [Google Scholar]
  12. Gao D-W, Wen Z-D. Phthalate esters in the environment: a critical review of their occurrence, biodegradation, and removal during wastewater treatment processes. Sci Total Environ 2016; 541:986–1001 [View Article] [PubMed]
    [Google Scholar]
  13. Cousins IT, Mackay D, Parkerton TF. Physical-chemical properties and evaluative fate modelling of phthalate esters. In Staples CA. eds Series Anthropogenic Compounds: The Handbook of Environmental Chemistry Berlin, Heidelberg: Springer; 2003 pp 57–84 [View Article]
    [Google Scholar]
  14. Lu Y, Tang F, Wang Y, Zhao J, Zeng X et al. Biodegradation of dimethyl phthalate, diethyl phthalate and di-n-butyl phthalate by Rhodococcus sp. L4 isolated from activated sludge. J Hazard Mater 2009; 168:938–943 [View Article] [PubMed]
    [Google Scholar]
  15. Fang HHP, Liang D, Zhang T. Aerobic degradation of diethyl phthalate by Sphingomonas sp. Bioresour Technol 2007; 98:717–720 [View Article] [PubMed]
    [Google Scholar]
  16. Fang C-R, Yao J, Zheng Y-G, Jiang C-J, Hu L-F et al. Dibutyl phthalate degradation by Enterobacter sp. T5 isolated from municipal solid waste in landfill bioreactor. Int Biodeterior Biodegrad 2010; 64:442–446 [View Article]
    [Google Scholar]
  17. Li J, Gu JD, Pan L. Transformation of dimethyl phthalate, dimethyl isophthalate and dimethyl terephthalate by Rhodococcus rubber Sa and modeling the processes using the modified Gompertz model. Int Biodeterior Biodegrad 2005; 55:223–232 [View Article]
    [Google Scholar]
  18. Tao Y, Li H, Gu J, Shi H, Han S et al. Metabolism of diethyl phthalate (DEP) and identification of degradation intermediates by Pseudomonas sp. DNE-S1. Ecotoxicol Environ Saf 2019; 173:411–418 [View Article] [PubMed]
    [Google Scholar]
  19. Zeng F, Cui K, Li X, Fu J, Sheng G. Biodegradation kinetics of phthalate esters by Pseudomonas fluoresences FS1. Process Biochem 2004; 39:1125–1129 [View Article]
    [Google Scholar]
  20. Ding J, Wang C, Xie Z, Li J, Yang Y et al. Properties of a newly identified esterase from Bacillus sp. K91 and its novel function in diisobutyl phthalate degradation. PLoS One 2015; 10:e0119216 [View Article] [PubMed]
    [Google Scholar]
  21. Boll M, Geiger R, Junghare M, Schink B. Microbial degradation of phthalates: biochemistry and environmental implications. Environ Microbiol Rep 2020; 12:3–15 [View Article] [PubMed]
    [Google Scholar]
  22. Feng N-X, Feng Y-X, Liang Q-F, Chen X, Xiang L et al. Complete biodegradation of di-n-butyl phthalate (DBP) by a novel Pseudomonas sp. YJB6. Sci Total Environ 2021; 761:143208 [View Article] [PubMed]
    [Google Scholar]
  23. Hu R, Zhao H, Xu X, Wang Z, Yu K et al. Bacteria-driven phthalic acid ester biodegradation: current status and emerging opportunities. Environ Int 2021; 154:106560 [View Article] [PubMed]
    [Google Scholar]
  24. Qiaofeng W, Jiabao Y. Degradation Kinetics and metabolic pathway of a strain for Di-N-butyl phthalate degrading. Fuel Chem Processes 2013; 44:41–44
    [Google Scholar]
  25. Zhang K, Liu Y, Chen Q, Luo H, Zhu Z et al. Biochemical pathways and enhanced degradation of di-n-octyl phthalate (DOP) in sequencing batch reactor (SBR) by Arthrobacter sp. SLG-4 and Rhodococcus sp. SLG-6 isolated from activated sludge. Biodegradation 2018; 29:171–185 [View Article] [PubMed]
    [Google Scholar]
  26. Wei S-S, Chen Y-L, Wu Y-W, Wu T-Y, Lai Y-L et al. Integrated multi-omics investigations reveal the key role of synergistic microbial networks in removing plasticizer Di-(2-Ethylhexyl) phthalate from estuarine sediments. mSystems 2021; 6:e0035821 [View Article] [PubMed]
    [Google Scholar]
  27. Mallick S, Chatterjee S, Dutta TK. A novel degradation pathway in the assimilation of phenanthrene by Staphylococcus sp. strain PN/Y via meta-cleavage of 2-hydroxy-1-naphthoic acid: formation of trans-2,3-dioxo-5-(2’-hydroxyphenyl)-pent-4-enoic acid. Microbiology 2007; 153:2104–2115 [View Article] [PubMed]
    [Google Scholar]
  28. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990; 215:403–410 [View Article] [PubMed]
    [Google Scholar]
  29. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 1997; 25:4876–4882 [View Article] [PubMed]
    [Google Scholar]
  30. Lowry OH, Rosebrough NJ, Farr AL, Randall RJ. Protein measurement with the Folin phenol reagent. J Biol Chem 1951; 193:265–275 [PubMed]
    [Google Scholar]
  31. James KD, Hughes MA, Williams PA. Cloning and expression of ntnD, encoding a novel NAD(P)+-independent 4-nitrobenzyl alcohol dehydrogenase from Pseudomonas sp. Strain TW3. J Bacteriol 2000; 182:3136–3141 [View Article] [PubMed]
    [Google Scholar]
  32. Sengupta S, Bhawsinghka N, Shaw R, Patra MM, Das Gupta SK. Mycobacteriophage D29 induced association of Mycobacterial RNA polymerase with ancillary factors leads to increased transcriptional activity. Microbiology 2022; 168:001158 [View Article] [PubMed]
    [Google Scholar]
  33. Rio DC, Ares M, Hannon GJ, Nilsen TW. Purification of RNA using TRIzol (TRI reagent). Cold Spring Harb Protoc 2010; 2010:pdb.prot5439 [View Article] [PubMed]
    [Google Scholar]
  34. Taghavi S, van der Lelie D, Mergeay M. Electroporation of Alcaligenes eutrophus with (mega) plasmids and genomic DNA fragments. Appl Environ Microbiol 1994; 60:3585–3591 [View Article] [PubMed]
    [Google Scholar]
  35. Deb S, Basu S, Singha A, Dutta TK. Development of a 2-Nitrobenzoate-Sensing Bioreporter Based on an Inducible Gene Cluster. Front Microbiol 2018; 9:254 [View Article] [PubMed]
    [Google Scholar]
  36. Heinaru E, Viggor S, Vedler E, Truu J, Merimaa M et al. Reversible accumulation of p-hydroxybenzoate and catechol determines the sequential decomposition of phenolic compounds in mixed substrate cultivations in pseudomonads. FEMS Microbiol Ecol 2001; 137:79–89 [View Article]
    [Google Scholar]
  37. Ornston LN, Stanier RY. The conversion of catechol and protocatechuate to 3-ketoadipate by Pseudomonas putida: I. Biochemistry. J Biol Chem 1966; 241:3776–3786 [View Article] [PubMed]
    [Google Scholar]
  38. Iwagami SG, Yang K, Davies J. Characterization of the protocatechuic acid catabolic gene cluster from Streptomyces sp. strain 2065. Appl Environ Microbiol 2000; 66:1499–1508 [View Article] [PubMed]
    [Google Scholar]
  39. Paul D, Chauhan A, Pandey G, Jain RK. Degradation of phydroxybenzoate via protocatechuate in Arthrobacter Protophormiae Rkj100 and Burkholderia Cepacia Rkj200. Curr Sci 2004; 87:1263–1268
    [Google Scholar]
  40. Ren L, Jia Y, Ruth N, Qiao C, Wang J et al. Biodegradation of phthalic acid esters by a newly isolated Mycobacterium sp. YC-RL4 and the bioprocess with environmental samples. Environ Sci Pollut Res 2016; 23:16609–16619 [View Article] [PubMed]
    [Google Scholar]
  41. Wang B, Wu S, Chang X, Chen J, Ma J et al. Characterization of a novel hyper-thermostable and chlorpyrifos-hydrolyzing carboxylesterase EstC: a representative of the new esterase family XIX. Pestic Biochem Physiol 2020; 170:104704 [View Article] [PubMed]
    [Google Scholar]
  42. Wang Y, Zhan W, Liu Y, Cheng S, Zhang C et al. Di-n-octyl phthalate degradation by a halotolerant bacterial consortium LF and its application in soil. Environ Technol 2021; 42:2749–2756 [View Article] [PubMed]
    [Google Scholar]
  43. Fan S, Wang J, Yan Y, Wang J, Jia Y. Excellent degradation performance of a versatile phthalic acid esters-degrading bacterium and catalytic mechanism of monoalkyl phthalate hydrolase. Int J Mol Sci 2018; 19:2803 [View Article] [PubMed]
    [Google Scholar]
  44. Jin D, Kong X, Liu H, Wang X, Deng Y et al. Characterization and genomic analysis of a highly efficient dibutyl phthalate-degrading bacterium Gordonia sp. strain QH-12. Int J Mol Sci 2016; 17:1012 [View Article] [PubMed]
    [Google Scholar]
  45. Han S-S, Kang HK, Jo BY, Ryu B-G, Jin HM et al. Complete genome sequence of Gordonia rubripertincta SD5, a soil bacterium isolated from a Di-(2-Ethylhexyl) phthalate-degrading enrichment culture. Microbiol Resour Announc 2020; 9:e01087-20 [View Article] [PubMed]
    [Google Scholar]
  46. Nahurira R, Wang J, Yan Y, Jia Y, Fan S et al. In silico genome analysis reveals the metabolic versatility and biotechnology potential of a halotorelant phthalic acid esters degrading Gordonia alkanivorans strain YC-RL2. AMB Express 2019; 9:21 [View Article] [PubMed]
    [Google Scholar]
  47. Li D, Yan J, Wang L, Zhang Y, Liu D et al. Characterization of the phthalate acid catabolic gene cluster in phthalate acid esters transforming bacterium-Gordonia sp. strain HS-NH1. Int Biodeterior Biodegrad 2016; 106:34–40 [View Article]
    [Google Scholar]
  48. Chatterjee S, Mallick S, Dutta TK. Pathways in the degradation of hydrolyzed alcohols of butyl benzyl phthalate in metabolically diverse Gordonia sp. strain MTCC 4818. J Mol Microbiol Biotechnol 2005; 9:110–120 [View Article] [PubMed]
    [Google Scholar]
  49. Huang H, Zhang X-Y, Chen T-L, Zhao Y-L, Xu D-S et al. Biodegradation of structurally diverse phthalate esters by a newly identified esterase with catalytic activity toward Di(2-ethylhexyl) phthalate. J Agric Food Chem 2019; 67:8548–8558 [View Article] [PubMed]
    [Google Scholar]
  50. Nishioka T, Iwata M, Imaoka T, Mutoh M, Egashira Y et al. A mono-2-ethylhexyl phthalate hydrolase from a Gordonia sp. that is able to dissimilate di-2-ethylhexyl phthalate. Appl Environ Microbiol 2006; 72:2394–2399 [View Article] [PubMed]
    [Google Scholar]
  51. Bhattacharyya M, Basu S, Dhar R, Dutta TK. Phthalate hydrolase: distribution, diversity and molecular evolution. Environ Microbiol Rep 2022; 14:333–346 [View Article] [PubMed]
    [Google Scholar]
  52. Wright RJ, Bosch R, Gibson MI, Christie-Oleza JA. Plasticizer degradation by marine bacterial isolates: a proteogenomic and metabolomic characterization. Environ Sci Technol 2020; 54:2244–2256 [View Article] [PubMed]
    [Google Scholar]
/content/journal/micro/10.1099/mic.0.001353
Loading
/content/journal/micro/10.1099/mic.0.001353
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error