Genomic and Transcriptomic Study for Screening Genes Involved in the Limonene Biotransformation of DSM 62840

Overview

Journal Front Microbiol

Specialty Microbiology

Date 2020 May 12

PMID 32390984

Citations 6

Authors

Lu-Lu Zhang

Wen Huang

Ying-Ying Zhang

Gang Fan

Jin He

Jing-Nan Ren

Zhi Li

Xiao Li

Si-Yi Pan

Affiliations

Soon will be listed here.

Abstract

α-Terpineol has been widely used in daily chemical, pharmaceutical, food, and flavor industries due to its pleasant odor with high economic value and pharmacological action. Our previous study showed that DSM 62840 was an efficient biocatalyst for the transformation of limonene to α-terpineol. Thus, it was meaningful to explore the genome features and the gene expression differences of strain DSM 62840 during limonene biotransformation, and the detailed bioconversion pathways. In this study, the functional genes related to limonene bioconversion were investigated using genome and transcriptome sequences analysis. The results showed that the DSM 62840 genome was estimated to be 29.09 Mb and it encoded 9,086 protein-encoding genes. The most annotated genes were associated to some protein metabolism and energy metabolism functions. When the threshold for differentially expressed genes (DEGs) was set at twofold ratio, a total of 4,128, and 4,148 DEGs were identified in P_L_12h (limonene-treated condition) compared with P_0h (blank) and P_12h (limonene-untreated blank), respectively. Among them, the expression levels of genes involved in the biosynthesis of secondary metabolites, energy metabolism and ATP-binding cassette (ABC) transporters were significantly altered during the biotransformation. And the reliability of these results was further confirmed by quantitative real-time polymerase chain reaction (RT-qPCR). Moreover, we found that the enzyme participated in limonene biotransformation was inducible. This enzyme was located in the microsome, and it was inhibited by cytochrome P450 inhibitors. This indicated that the cytochrome P450 may be responsible for the limonene bioconversion. Several differentially expressed cytochrome P450 genes were further identified, such as PDIDSM_85260 and PDIDSM_67430, which were significantly up-regulated with limonene treatment. These genes may be responsible for converting limonene to α-terpineol. Totally, the genomic and transcriptomic data could provide valuable information in the discovery of related-genes which was involved in limonene biotransformation, pathogenicity of fungi, and investigation of metabolites and biological pathways of strain DSM 62840.

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References

Hassan S, Gali-Muhtasib H, Goransson H, Larsson R . Alpha terpineol: a potential anticancer agent which acts through suppressing NF-kappaB signalling. Anticancer Res. 2010; 30(6):1911-9. View

Wang Y, Lim L, DiGuistini S, Robertson G, Bohlmann J, Breuil C . A specialized ABC efflux transporter GcABC-G1 confers monoterpene resistance to Grosmannia clavigera, a bark beetle-associated fungal pathogen of pine trees. New Phytol. 2012; 197(3):886-898. DOI: 10.1111/nph.12063. View

Bier M, Bianchi Pedroni Medeiros A, Soccol C . Biotransformation of limonene by an endophytic fungus using synthetic and orange residue-based media. Fungal Biol. 2017; 121(2):137-144. DOI: 10.1016/j.funbio.2016.11.003. View

Held S, Schieberle P, Somoza V . Characterization of alpha-terpineol as an anti-inflammatory component of orange juice by in vitro studies using oral buccal cells. J Agric Food Chem. 2007; 55(20):8040-6. DOI: 10.1021/jf071691m. View

Love M, Huber W, Anders S . Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014; 15(12):550. PMC: 4302049. DOI: 10.1186/s13059-014-0550-8. View

Julca I, Droby S, Sela N, Marcet-Houben M, Gabaldon T . Contrasting Genomic Diversity in Two Closely Related Postharvest Pathogens: Penicillium digitatum and Penicillium expansum. Genome Biol Evol. 2015; 8(1):218-27. PMC: 4758248. DOI: 10.1093/gbe/evv252. View

Burger G, Strauss J, Scazzocchio C, Lang B . nirA, the pathway-specific regulatory gene of nitrate assimilation in Aspergillus nidulans, encodes a putative GAL4-type zinc finger protein and contains four introns in highly conserved regions. Mol Cell Biol. 1991; 11(11):5746-55. PMC: 361946. DOI: 10.1128/mcb.11.11.5746-5755.1991. View

Zheng S, Jing G, Wang X, Ouyang Q, Jia L, Tao N . Citral exerts its antifungal activity against Penicillium digitatum by affecting the mitochondrial morphology and function. Food Chem. 2015; 178:76-81. DOI: 10.1016/j.foodchem.2015.01.077. View

Bavishi K, Li D, Eiersholt S, Hooley E, Petersen T, Moller B . Direct observation of multiple conformational states in Cytochrome P450 oxidoreductase and their modulation by membrane environment and ionic strength. Sci Rep. 2018; 8(1):6817. PMC: 5931563. DOI: 10.1038/s41598-018-24922-x. View

10.

Munday S, Maddigan N, Young R, Bell S . Characterisation of two self-sufficient CYP102 family monooxygenases from Ktedonobacter racemifer DSM44963 which have new fatty acid alcohol product profiles. Biochim Biophys Acta. 2016; 1860(6):1149-62. DOI: 10.1016/j.bbagen.2016.01.023. View

11.

Sun X, Li H, Yu D . Complete mitochondrial genome sequence of the phytopathogenic fungus Penicillium digitatum and comparative analysis of closely related species. FEMS Microbiol Lett. 2011; 323(1):29-34. DOI: 10.1111/j.1574-6968.2011.02358.x. View

12.

Woloshuk C, Foutz K, Brewer J, Bhatnagar D, Cleveland T, Payne G . Molecular characterization of aflR, a regulatory locus for aflatoxin biosynthesis. Appl Environ Microbiol. 1994; 60(7):2408-14. PMC: 201664. DOI: 10.1128/aem.60.7.2408-2414.1994. View

13.

Skene D, Papagiannidou E, Hashemi E, Snelling J, Lewis D, Fernandez M . Contribution of CYP1A2 in the hepatic metabolism of melatonin: studies with isolated microsomal preparations and liver slices. J Pineal Res. 2001; 31(4):333-42. DOI: 10.1034/j.1600-079x.2001.310408.x. View

14.

Makovec T, Breskvar K . Purification of cytochrome P450 from filamentous fungus Rhyzopus nigricans. Pflugers Arch. 2017; 439(Suppl 1):r111-r112. DOI: 10.1007/s004240000110. View

15.

Lin Y, Lin H, Chen Y, Wang H, Lin M, Ritenour M . The role of ROS-induced change of respiratory metabolism in pulp breakdown development of longan fruit during storage. Food Chem. 2019; 305:125439. DOI: 10.1016/j.foodchem.2019.125439. View

16.

Ali M, Li X, Tang Q, Liu X, Chen F, Xiao J . Regulation of Inducible Potassium Transporter KdpFABC by the KdpD/KdpE Two-Component System in . Front Microbiol. 2017; 8:570. PMC: 5401905. DOI: 10.3389/fmicb.2017.00570. View

17.

Yu F, Song J, Liang J, Wang S, Lu J . Whole genome sequencing and genome annotation of the wild edible mushroom, Russula griseocarnosa. Genomics. 2019; 112(1):603-614. DOI: 10.1016/j.ygeno.2019.04.012. View

18.

Vedula L, Zhao Y, Coates R, Koyama T, Cane D, Christianson D . Exploring biosynthetic diversity with trichodiene synthase. Arch Biochem Biophys. 2007; 466(2):260-6. PMC: 2036078. DOI: 10.1016/j.abb.2007.06.016. View

19.

Baba S, Nihira T, Hosobuchi M . Identification of the specific sequence recognized by Penicillium citrinum MlcR, a GAL4-type transcriptional activator of ML-236B (compactin) biosynthetic genes. Fungal Genet Biol. 2008; 45(9):1277-83. DOI: 10.1016/j.fgb.2008.07.002. View

20.

Traven A, Jelicic B, Sopta M . Yeast Gal4: a transcriptional paradigm revisited. EMBO Rep. 2006; 7(5):496-9. PMC: 1479557. DOI: 10.1038/sj.embor.7400679. View