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A Bacterium That Degrades and Assimilates Poly(Ethylene Terephthalate)

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A Bacterium That Degrades and Assimilates Poly(Ethylene Terephthalate) 1 Title: A bacterium that degrades and assimilates poly(ethylene terephthalate) 2 † 3 Authors: Shosuke Yoshida1,2 , Kazumi Hiraga1, Toshihiko Takehana3, Ikuo Taniguchi4, 4 Hironao Yamaji1, Yasuhito Maeda5, Kiyotsuna Toyohara5, Kenji Miyamoto2*, Yoshiharu 5 Kimura4, & Kohei Oda1* 6 Affiliations: 7 1Department of Applied Biology, Faculty of Textile Science, Kyoto Institute of Technology, 8 Matsugasaki, Sakyo-ku, Kyoto .0.-0 0 , 1apan 9 2Department of Biosciences and Informatics, Keio 2ni3ersity, 3-14-1 Hiyoshi, Kohoku-ku, 10 Yokohama, Kanagawa 223-0 22, 1apan 11 35ife Science Materials 5aboratory, ADEKA Corporation, 7-2-34 Higashiogu, Arakawa-ku, 12 Tokyo 11.-0 3, 1apan 13 4Department of Polymer Science, Faculty of Te,tile Science, Kyoto Institute of Technology, 14 Matsugasaki, Sakyo-ku, Kyoto .0.-0 0 , 1apan 15 Ecology-Related Material Group Inno3ation Research Institute, Teijin 5td., Hinode-cho 2-1, 16 Iwakuni, Yamaguchi 740-0 11, 1apan 17 Current address: Department of Polymer Chemistry, Graduate School of Engineering, Kyoto 18 2ni3ersity, Nishikyo-ku, Kyoto .1 -0 30, 1apan 19 "Correspondence to: K.M. (kmiyamotoAbio.keio.ac.jp) or K.O. (bikaAkit.ac.jp). 20 21 1 22 Abstract: Poly(ethylene terephthalate) (PET) is used e,tensi3ely worldwide in plastic products, 23 and its accumulation in the en3ironment has become a global concern. Because the ability to 24 enzymatically degrade PET for microbial growth has been limited to a few fungal species, 25 biodegradation is not yet a 3iable remediation or recycling strategy. By screening natural 26 microbial communities e,posed to PET in the en3ironment, we isolated a no3el bacterium, 27 Ideonella sakaiensis 201-F., that is able to utilize PET as its major energy and carbon source. 28 Chen grown on PET, this strain produces two enzymes capable of hydrolyzing PET and the 29 reaction intermediate, mono(2-hydro,yethyl) terephthalic acid (MHET). Both enzymes are 30 reDuired to enzymatically con3ert PET efficiently into its two en3ironmentally benign monomers, 31 terephthalic acid and ethylene glycol. 32 33 Main Text: Plastics with desirable properties such as durability, plasticity, andEor transparency 34 ha3e been industrialized o3er the last century and widely incorporated into countless consumer 35 products (1). Many of these products are remarkably persistent in the en3ironment due to the 36 absence or low acti3ity of catabolic enzymes that might otherwise break down their plastic 37 constituents. In particular, polyesters containing a high ratio of aromatic components, such as 38 poly(ethylene terephthalate) (PET), are chemically inert, resulting in resistance to microbial 39 degradation (2, 3). Appro,imately . million tons of PET was produced worldwide in 2013 40 alone, prompting further industrial production of its monomers, terephthalic acid (TPA) and 41 ethylene glycol (EG), both of which are deri3ed from raw petroleum. 5arge Duantities of PET 42 ha3e been introduced into the en3ironment through its production and disposal, resulting in the 43 accumulation of PET in en3ironments across the globe (4). 2 44 There are 3ery few reports on the biological degradation of PET or its utilization to 45 support microbial growth. Rare e,amples include members of the filamentous fungi Fusarium 46 oxysporum and F. solani, that can grow on a mineral medium containing PET yarns Falthough no 47 growth le3els were specifiedG (5, 6). Once identified, microorganisms ha3ing enzymatic 48 machinery to degrade PET could ser3e as an en3ironmental remediation strategy as well as a 49 degradationEfermentation platform for biological recycling of PET waste products. 50 Ce collected 2 0 PET debris-contaminated en3ironmental samples including sediment, 51 soil, wastewater, and acti3ated sludge from a PET-bottle recycling site (7). 2sing these samples, 52 we screened for microorganisms that could use low crystallinity (1.9I) PET film as the major 53 carbon source for growth. One sediment sample contained a distinct microbial consortium that 54 formed on the PET film upon culturing (Fig. 1A) and induced morphological change of the PET 55 film (Fig. 1B). Microscopy re3ealed that the consortium on the film, termed JNo. 4.K, contained 56 a mi,ture of bacteria, yeast-like cells, and protozoa, whereas the culture fluid was almost 57 transparent (Fig. 1A). This consortium degraded the PET film surface (Fig. S1) at a rate of 0.13 58 mgEcm2Eday at 30LC (Fig. 1C). Se3enty-fi3e percent of the degraded PET film carbon was 59 catabolized into CO2 at 20LC (Fig. S2). 60 2sing limiting dilutions of consortium No. 4. that were cultured with PET film to enrich 61 for microorganisms nutritionally dependent on PET, we successfully isolated a bacterium 62 capable of degrading and assimilating PET. The strain represents a no3el species of the genus 63 Ideonella, for which we propose the name Ideonella sakaiensis 201-F. (NCBI ta,onomy 64 database, ID: 1 47922). In addition to being found in the culture fluid, cells were obser3ed on 65 the film (Fig. 1D) and appeared to be connected to each other by appendages (Fig. 1E). Shorter 66 appendages were obser3ed between the cells and the film and these might assist deli3ery of 3 67 secreted enzymes into the film (Fig. 1, D and F). The PET film was damaged e,tensi3ely (Fig. 68 1G) and almost completely degraded after . weeks at 30LC (Fig. 1H). In the course of 69 subculturing No. 4., we found a consortium that lost its PET degradation capability. This 70 consortium lacked I. sakaiensis (Fig. S3), indicating that this strain is functionally in3ol3ed in 71 PET degradation within the consortium. 72 There are currently 3ery few e,amples of esterases, lipases, or cutinases that are capable 73 of hydrolyzing PET (8, 9). To e,plore the genes in3ol3ed in PET hydrolysis in I. sakaiensis 201- 74 F., we assembled a draft seDuence of its genome (Table S1). One gene (ISF._4031) was 75 identified that encodes a putati3e lipase sharing 1I amino acid seDuence identity and catalytic 76 residues with a hydrolase from Thermo ifida fusca (TfH) (Table S2 and Fig. S4), and which 77 e,hibits PET-hydrolytic acti3ity (10). Ce purified the corresponding recombinant I. sakaiensis 78 proteins (Fig. S ) and incubated them with PET film at 30LC for 10 h. Prominent pitting 79 de3eloped on the film surface (Fig. 2A). Mono(2-hydro,yethyl) terephthalic acid (MHET) was 80 the major product released by the recombinant protein, together with minor amounts of TPA and 81 bis(2-hydro,yethyl) TPA (BHET) (Fig. 2B). These results suggested that the ISF._4031 protein 82 hydrolyzes PET. This protein also hydrolyzed BHET to yield MHET with no further 83 decomposition. 84 Ce compared the acti3ity of the ISF._4031 protein to that of three e3olutionarily 85 di3ergent PET-hydrolytic enzymes identified from a phylogenetic tree constructed using 86 published enzymes (Fig. 2C and Table S2). Ce purified TfH from a thermophilic actinomycete 87 (10), 5C-cutinase (5CC) from a compost metagenome (11), and F. solani cutinase (FsC) from a 88 fungus (12) (Fig. S ), and measured their acti3ities against para-nitrophenol (pNP)-linked 89 aliphatic esters, PET film, and BHET at 30LC, pH 7.0. For pNP-aliphatic esters, that are 4 90 preferred by lipases and cutinases, the acti3ity of the ISF._4031 protein was lower than that of 91 TfH, 5CC, and FsC (Fig. 2D). The acti3ity of the ISF._4031 protein against the PET film, 92 howe3er, was 120-, . -, and 00-fold higher than that of TfH, 5CC, and FsC, respecti3ely. A 93 similar trend was obser3ed for BHET (Fig. 2D). The catalytic preference of the ISF._4031 94 protein for PET film 3ersus pNP-aliphatic esters was also substantially higher than that of TfH, 95 5CC, and FsC (300-, 40-, and 400-fold on a3erage, respecti3ely) (Fig. 2D). Thus, the ISF._4031 96 protein preferred PET to aliphatic esters, compared with the other enzymes, leading to its 97 designation as a PET hydrolase (PETase). 98 PETase was also more acti3e than TfH, 5CC, and FsC against commercial bottle-deri3ed 99 PET, which is highly crystallized (Fig. 2E), e3en though the densely packed structure of highly 100 crystallized PET greatly reduces enzymatic hydrolysis of its ester linkages (9, 13). PETase was 101 somewhat heat-labile, but remarkably more acti3e against PET film at low temperatures than 102 TfH, 5CC, and FsC (Fig. 2F). Enzymatic degradation of polyesters is controlled mainly by their 103 chain mobility (14). Fle,ibility of the polyester chain decreases as the glass transition 104 temperature (Tg) increases (9). The Tg of PET is around 7 LCN i.e. the polyester chain of PET is 105 in a glassy state at moderate temperatures appropriate for mesophilic enzyme reactions. The 106 substrate specificity of PETase, and its prominent hydrolytic acti3ity for PET in a glassy state, 107 would be critical to sustaining growth of this strain on PET in most en3ironments where PET 108 products e,ist. 109 I. sakaiensis adheres to PET (Fig. 1DOF) and secretes PETase to target this material. Ce 110 compared the PET hydrolytic acti3ity of PETase with that of the other three PET hydrolytic 111 enzymes (Fig. S7). The acti3ity ratios of PETase 3ersus the other enzymes decreased as the 112 enzyme concentrations increased, indicating that PETase efficiently hydrolyzed PET with less 5 113 enzyme diffusion into the aDueous phase andEor plastic 3essels used for the reaction. PETase 114 lacks apparent substrate-binding motif(s) such as carbohydrate binding modules generally 115 obser3ed in glycoside hydrolases. Therefore, without the 3D structure of PETase, the e,act 116 binding mechanism is unknown. 117 MHET, the product of PETase-mediated hydrolysis of BHET and PET, was an e,tremely 118 minor component in the supernatant of I. sakaiensis cultured on PET film (Fig.
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