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Prediction and Identification of Biochemical Pathway of Acteoside from Whole Genome Sequences of Abeliophyllum Distichum Nakai, Cultivar Ok Hwang 1Ho

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Prediction and Identification of Biochemical Pathway of Acteoside from Whole Genome Sequences of Abeliophyllum Distichum Nakai, Cultivar Ok Hwang 1Ho Journal of Convergence for Information Technology e-ISSN 2586-4440 Vol. 10. No. 3, pp. 76-91, 2020 DOI : https://doi.org/10.22156/CS4SMB.2020.10.03.076 Prediction and Identification of Biochemical Pathway of Acteoside from Whole Genome Sequences of Abeliophyllum Distichum Nakai, Cultivar Ok Hwang 1ho Jaeho Park1, Hong Xi2, Jiyun Han3, Jeongmin Lee3, Yongsung Kim4, Jun-mi Lee3, Janghyuk Son5, Joungjwa Ahn6, Taewon Jang7, Jisoo Choi8, Jongsun Park5* 1Professor, Department of Pharmaceutical Science, JungWon University 2Senior Researcher, InfoBoss Co., Ltd. & InfoBoss Research Center 3Researcher, InfoBoss Co., Ltd. & InfoBoss Research Center 4Team Leader, InfoBoss Co., Ltd. & InfoBoss Research Center 5CEO, InfoBoss Co., Ltd. & InfoBoss Research Center 6Professor, Department of Food Science & Technology, JungWon University 7Student, Department of Medicinal Plant Resources, Andong National University 8Student, Department of Pharmaceutical Science, JungWon University 미선나무 품종 옥황 1호의 유전체를 활용한 Acteoside 생화학 합성과정 예측 및 확인 박재호1, 시 홍2, 한지윤3, 이정민3, 김용성4, 이준미3, 손장혁5, 안정좌6, 장태원7, 최지수8, 박종선5* 1중원대학교 제약공학과 교수, 2인포보스 주식회사 및 인포보스 기업부설연구소 선임연구원, 3인포보스 주식회사 및 인포보스 기업부설연구소 연구소 연구원, 4인포보스 주식회사 및 인포보스 기업부설연구소 팀장, 5인포보스 주식회사 및 인포보스 기업부설연구소 대표, 6중원대학교 식품공학과 교수, 7안동대학교 생약자원개발학과 학생, 8중원대학교 제약공학과 학생 Abstract Whole genome sequence of Abeliophyllum distichum Nakai (Oleaceae) cultivar Ok Hwang 1 Ho, which is Korean endemic species, was recently sequenced to understand its characteristics. Acteoside is one of major useful compounds presenting various activities, and its several proposed biochemical pathways were reviewed and integrated to make precise biochemical pathway. Utilizing MetaPre-AITM which was developed for predicting secondary metabolites based on whole genome with the precise biochemical pathway of acteoside and the InfoBoss Pathway Database, we successfully rescued all enzymes involved in this pathway from the genome sequences, presenting that A. distichum cultivar Ok Hwang 1 Ho may produce acteoside. High-performance liquid chromatography result displayed that callus of A. distichum cultivar Ok Hwang 1 Ho contained acteoside as well as isoacteoside which may be derived from acteoside. Taken together, we successfully showed that MetaPre-AITM can predict secondary metabolite from plant whole genomes. In addition, this method will be efficient to predict secondary metabolites of many plant species because DNA can be analyzed more stability than chemical compounds. Key Words : Acteoside, biochemical pathway, Whole genome, MetaPre-AITM, InfoBoss Pathway Database, Abeliophyllum distichum, cultivar Ok Hwang 1ho 요 약 최근에 한국 고유종인 미선나무 (Abeliophyllum distichum Nakai; Oleaceae) 품종 옥황1호의 유전체가 성공적으로 해독되었다. Acteoside는 다양한 활성을 가지는 물질이며, 여러개의 생화학합성과정이 제시되어왔고, 이들을 통합 검토하여 정 확한 생화학합성과정을 완성하였다. 유전체 데이터로부터 2차대사산물을 예측할 수 있는 MetaPre-AITM와 정확한 acteoside 생화학합성과정, InfoBoss Pathway Database를 활용하여, acteoside에 관여하는 모든 효소의 유전자를 옥황1호 유전체로부 터 성공적으로 확인하였다. 이는 옥황1호는 acteoside 물질을 생산할 수 있는 가능성이 있음을 의미한다. 이에 고성능액체크로 마토그래피를 사용하여 옥황1호의 캘러스 세포를 분석하여 acteoside과 이의 유도체인 isoacteoside를 확인하였다. 본 연구는 MetaPre-AITM은 유전체로부터 2차대사산물을 성공적으로 예측하였다. 이 방법은 화학물질보다 안정적인 DNA를 분석하여 2 차 대사산물을 예측하는 효율적인 방법이 될 것이다. 주제어 : Acteoside, 생화학 합성과정, 유전체, MetaPre-AITM, InfoBoss Pathway Database, Abeliophyllum distichum, 옥황1호 *This study was fully supported by the InfoBoss Research Grant(IBG-0032). *Corresponding Author : Jongsun Park([email protected]) Received January 6, 2020 Revised February 6, 2020 Accepted March 20, 2020 Published March 28, 2020 77 융합정보논문지 제10권 제3호 1. Background background is identical, which is good for controlling quality. Ok Hwang 1ho has already Abeliophyllum distichum Nakai belonging to been cultivated for long time in Oleaceae is Korean endemic species in GoesanBunjae-Nongwon (Goesan-gun, Chungbuk Abeliophyllum genus unique in Korea. This Province, Republic of Korea). Genome sequence genus is independent to neighbor genus, of A. distichum cultivar Ok Hwang 1ho can be Forsythia, based on phylogenetic studies [1,2] as used for finding enzymes involved in biochemical well as complete chloroplast genome sequences pathways of secondary metabolites. One of [2-6]. It indicates that A. distichum is one of typical examples is Coffea canephora genome economically valuable our own biological for identifying caffeine biosynthesis: all resources under the Nagoya Protocol [7]. Till identified enzymes of this biochemical pathway now, ten natural habitats have been reported were identified from genome sequences and [8-11], which is a limited factor to prepare compared with the other species [24]. In enough amount of samples for extracting useful addition, tea (Camellia sinensis) genome was compounds. However, commercial cultivar, also sequenced with presenting enzymes of named as Ok Hwang 1ho, was successfully caffeine biosynthesis pathway [25]. registered and cultivated well, indicating that Acteoside, which is a caffeoyl phenylethanoid enough amount of samples can be prepared for glycoside isolated from various Lamiales plant commercial use. species including Phlomis genus (Lamiaceae) Recent researches have reported that A. [26], Byblis liniflora (Byblidaceae) [27], distichum synthesize acteoside, eutigoside B, Verbascum phlomoides [28], Verbascum isoacteoside, rutin, cornoside, and hirsutrin [12, mallophorum (Scrophulariaceae) [29], Plantago 13]. Moreover, activities of extracts from A. lanceolata (Plantaginaceae) [30], Plantago distichum have been investigated showing asiatica (Plantaginaceae) [31], and Rehmannia anti-cancer activity [14,15], antioxidative glutinosa (Orobanchaceae) [32], plays multiple activities [16-20], inhibition of DNA damage roles as a neuroprotective agent [33-35], an [16,21], anti-inflammatory effects [15,17,19,22], anti-inflammatory agent [36-38], an and whiting effect of skin [18,20,23]. These results antibacterial agent [36,39-41], and an antiviral strongly support that A. distichum is a good activity [31]. target to understand its usefulness as candidate In this study, we investigated three biochemical of medical materials and functional foods. In pathways of acteoside described in Fig. 1 and addition, these compounds and activities were proposed the integrated biochemical pathway identified in natural isolate of A. distichum. described in Fig. 2 Based on this pathway, we Recently, whole genome of A. distichum successfully identified the enzyme genes from cultivar Ok Hwang 1ho was successfully genome sequence of A. distichum cultivar Ok Hwang sequenced and assembled, presenting 1.01 Gbp 1ho collected from GoesanBunjae-Nongwon in length which is congruent to the result of (Goesan-gun, Chungbuk Province, Republic of k-mer analysis (1.02 Gbp; Park et al., in Korea) with utilizing MetaPre-AITM. Based on preparation). Official cultivar of A. distichum has prediction result, in total, 42 predicted genes two advantages: amount of plant samples can be were mapped to 24 enzymes in the three easily expanded based on already accumulated proposed pathways and 33 predicted genes cultivation experiences and its genetic Prediction and Identification of Biochemical Pathway of Acteoside from Whole Genome Sequences of Abeliophyllum Distichum Nakai, Cultivar Ok Hwang 1ho 78 corresponding to 17 enzymes from the acteoside, the bioinformatic pipeline, named as integrated pathway of acteoside were MetaPre-AITM, was used, which was constructed successfully identified from the genome of A. together with the GenomeArchive® distichum cultivar Ok Hwang 1ho. After that we (http://www.genomearchive.info/; Park et al., in confirmed existence of acteoside in callus of A. preparation), the Genome Information System (GiS; distichum cultivar Ok Hwang 1ho via http://gis.infoboss.co.kr/), and the InfoBoss Pathway high-performance liquid chromatography Database (IPD; http://pathway.infoboss.co.kr/; Park experiment. Our results strongly suggested that et al., in preparation). IPD is a standardized plant secondary metabolites can be predicted database of curated biochemical pathways with from the genome sequences with the plant genomes supported by the Plant Genome MetaPre-AITM. Database (http://www.plantgenome.info; Park et al., in preparation). MetaPre-AITM contains three major 2. Materials & Methods components to identify enzymes from whole genome sequences as depicted in Fig. 3: i) 2.1 Preparation of callus of A. distichum homology-based enzyme identifier which selects cultivar Ok Hwang 1ho candidate genes based on already-known enzyme Fresh leaves of A. distichum cultivar Ok Hwang amino acid sequences, ii) functional-domain based 1ho were collected from GoesanBunjae-Nongwon enzyme identifier which utilizes functional domains (Goesan-gun, Chungbuk Province, Republic of predicted by InterProScan [42], iii) Korea, Voucher in InfoBoss Cyber Herbarium (IN); phylogenetic-approach enzyme identifier which Y. Kim, IB-00589). Leaves were surface sterilized finds correct enzymes which display high similarity for 3 sec in 70% ethanol, soaked in sodium of amino acids within gene family, such as hypochlorite (5.25%), 10 min in sterile aquadest Cytochrome P450s, iv) amino acid pattern analyzer and then they were washed two times with sterile based on support vector machine (SVM) which aquadest in laminar air-flow hood. The callus classifies enzymes with forth-level of enzyme induction media was composed of MS (Murashige classification (EC) numbers displaying better than and Skoog) basal medium and supplemented with previous AI-based classifiers [43, 44], and v) 30 g/L sucrose, naphthalene acetic acid 1 mg/L,
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