Trans-omic study for diversity and evolution of venomic proteins of Protobothrops flavoviridis.

• Project/Area Number: 18H02498
• Research Category: Grant-in-Aid for Scientific Research (B)
• Allocation Type: Single-year Grants
• Section: 一般
• Review Section: Basic Section 45030:Biodiversity and systematics-related
• Research Institution: Kyushu University
• Principal Investigator: Shibata Hiroki 九州大学, 生体防御医学研究所, 准教授 (80315093)
• Co-Investigator(Kenkyū-buntansha): 小川 智久 東北大学, 農学研究科, 教授 (80240901)
• Project Period (FY): 2018-04-01 – 2022-03-31
• Project Status: Completed (Fiscal Year 2021)
• Budget Amount: ¥17,290,000 (Direct Cost: ¥13,300,000、Indirect Cost: ¥3,990,000); Fiscal Year 2021: ¥2,730,000 (Direct Cost: ¥2,100,000、Indirect Cost: ¥630,000); Fiscal Year 2020: ¥4,160,000 (Direct Cost: ¥3,200,000、Indirect Cost: ¥960,000); Fiscal Year 2019: ¥4,680,000 (Direct Cost: ¥3,600,000、Indirect Cost: ¥1,080,000); Fiscal Year 2018: ¥5,720,000 (Direct Cost: ¥4,400,000、Indirect Cost: ¥1,320,000)
• Keywords: 遺伝的多様性 / ハブ / 毒液タンパク質 / 加速進化 / 系統地理学 / 毒液 / 蛇毒

Outline of Final Research Achievements

The whole genome assembly of habu individuals from four populations, Amami (Protobothrops flavoviridis), Okinawa (P. flavoviridis), Kodakara (P. tokarensis) and Iriomote (P. elegans) revealed different structures in gene clusters of venom protein gene families such as metalloproteinase and C-type lectin genes (supported by JSPS KAKENHI Grant Number 22H04925 (PAGS)). We also obtained mtDNA sequences from 150 individuals from 14 populations and evaluated the genetic divergence and migrations among the populations. 2D analyses of venoms from 47 individuals from 9 populations showed different expression pattern between populations as well as within populations, while RNAseq of venom glands showed no clear difference in expression levels of venom protein genes between populations. These observations suggest that the difference in protein expression levels in venoms can be attributed to genomic, translational and post-translational levels rather than transcriptional levels.

Academic Significance and Societal Importance of the Research Achievements

本研究計画で行った複数集団のハブの全ゲノム、毒腺トランスクリプトームおよび毒液プロテオーム解析から、毒液タンパク質発現の集団間多様性は、遺伝子クラスター構造の差異によって生じることに加えて、翻訳/修飾レベルでも生じている可能性が示唆され、既報告の加速進化や選択的スプライシングに加えて（Shibata et al. 2018; Ogawa et al. 2019）、毒液タンパク質の多様化をもたらす新たな機構と考えられた。さらに、集団遺伝学的解析のために取得した14島からの計150個体についてのmtDNAの変異情報は、今般の「奄美・沖縄」の世界自然遺産登録後の環境保全に資する基盤的データとなった。

Research Products

• [Journal Article] Active Expression of Genes for Protein Modification Enzymes in the Venom Gland of Habu Snakes. (2022)
  • Author(s): Isomoto A, Shoguchi E, Hisata K, Inoue J, K, Sun Y, Inaba K, Satoh N, Ogawa T, Shibata H.
  • Journal Title: Toxins Volume: 14 Pages: 300-300
  • Peer Reviewed
• [Journal Article] Venomics Study of <i>Protobothrops flavoviridis</i> Snake: How Venom Proteins Have Evolved and Diversified? (2020)
  • Author(s): Ogawa Tomohisa、Shibata Hiroki
  • Journal Title: Medical Toxicology Volume: -
  • DOI: 10.5772/intechopen.91960
  • ISBN: 9781838802776, 9781838802783
• [Journal Article] The Indian cobra reference genome and transcriptome enables comprehensive identification of venom toxins (2020)
  • Author(s): Suryamohan K, Krishnankutty SP, Guillory J, Jevit M, Schroeder M, Wu M et al.
  • Journal Title: Nature Genetics Volume: 52 Issue: 1 Pages: 106-117
  • DOI: 10.1038/s41588-019-0559-8
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Discovery of the Gene Encoding a Novel Small Serum Protein (SSP) of Protobothrops flavoviridis and the Evolution of SSPs (2020)
  • Author(s): Inamaru Kento、Takeuchi Ami、Maeda Marie、Shibata Hiroki、Fukumaki Yasuyuki、Oda-Ueda Naoko、Hattori Shosaku、Ohno Motonori、Chijiwa Takahito
  • Journal Title: Toxins Volume: 12 Issue: 3 Pages: 177-177
  • DOI: 10.3390/toxins12030177
  • Peer Reviewed / Open Access
• [Journal Article] Unique structure (construction and configuration) and evolution of the array of small serum protein genes of Protobothrops flavoviridis snake (2019)
  • Author(s): Chijiwa T, Inamaru K, Takeuchi A, Maeda M, Yamaguchi K, Shibata H, Hattori S, Oda-Ueda N, Ohno M.
  • Journal Title: Bioscience Reports Volume: 39 Issue: 7
  • DOI: 10.1042/bsr20190560
  • Peer Reviewed
• [Journal Article] Alternative mRNA Splicing in Three Venom Families Underlying a Possible Production of Divergent Venom Proteins of the Habu Snake, Protobothrops flavoviridis (2019)
  • Author(s): Ogawa T, Oda-Ueda N, Hisata K, Nakamura H, Chijiwa T, Hattori S, Isomoto A, Yugeta H, Yamasaki S, Fukumaki Y, Ohno M, Satoh N, Shibata H
  • Journal Title: Toxins Volume: 11 Issue: 10 Pages: 581-581
  • DOI: 10.3390/toxins11100581
  • Peer Reviewed
• [Journal Article] An albino mutant of the Japanese rat snake (<i>Elaphe climacophora</i>) carries a nonsense mutation in the tyrosinase gene (2018)
  • Author(s): Iwanishi S, Zaitsu S, Shibata H, Nitasaka E.
  • Journal Title: Genes & Genetic Systems Volume: 93 Issue: 4 Pages: 163-167
  • DOI: 10.1266/ggs.18-00021
  • NAID: 130007503883
  • ISSN: 1341-7568, 1880-5779
  • Year and Date: 2018-08-01
  • Peer Reviewed
• [Journal Article] The habu genome reveals an evolutionary background of venom protein genes. (2018)
  • Author(s): Shibata H, Chijiwa T, Oda-Ueda N, Nakamura H, Yamaguchi K, Hattori S, Matsubara K, Matsuda Y, Yamashita A, Isomoto A, Mori K, Tashiro K, Kuhara S, Yamasaki S, Fujie M, Goto H, Koyanagi R, Takeuchi T, Fukumaki Y, Ohno M, Shoguchi E, Hisata K, Satoh N, Ogawa T.
  • Journal Title: Sci Rep. Volume: 8 Issue: 1 Pages: 11300-11300
  • DOI: 10.1038/s41598-018-28749-4
  • Peer Reviewed / Open Access
• [Presentation] 南西諸島14島からの109個体を用いたハブの集団構造解析 (2021)
  • Author(s): 比留木 成美、手島 康介、寺田 考紀、服部 正策、柴田 弘紀
  • Organizer: 日本遺伝学会第93回大会、学習院大学目白キャンパス
• [Presentation] 人工抗毒素産生系開発に向けた抗毒素のレパトア解析 (2021)
  • Author(s): 孫 崟瑞、範 駱鳴、小川 智久、柴田 弘紀
  • Organizer: 第67回トキシンシンポジウム、バーチャルシンポジウム
• [Presentation] 比較ゲノミクスとタンパク質構造予測から推定されたヘビSmall Serum Proteins（SSPs）の進化 (2021)
  • Author(s): 稲丸 賢人、竹内 亜美、前田 真理恵、柴田 弘紀、服巻 保幸、上田 直子、服部 正策、大野 素徳、千々岩 崇仁
  • Organizer: 第43回日本分子生物学会年会、パシフィコ横浜
• [Presentation] Diversity and evolution of venom protein genes of a Japanese endemic pit viper, habu, Protobothrops flavoviridis. (2019)
  • Author(s): Shibata H.
  • Organizer: The 1st NUS-FU-KU Joint Symposium on Biochemistry in FUKUOKA, Fukuoka University, Fukuoka, Japan
  • Int'l Joint Research / Invited
• [Presentation] Habu snake (Protobothrops flavoviridis) genome study: Genomic architecture implicated in the multiplication and accelerated evolution of venom protein. (2019)
  • Author(s): Shibata H, Oda-Ueda N, Chijiwa T, Nakamura H, Yamaguchi K, Hattori S, Matsubara K, Matsuda Y, Koyanagi R, Fukumaki Y, Ohno M, Shoguchi E, Satoh N, Ogawa T.
  • Organizer: EMBO/EMBL Symposium: Systems Genetics: From Genomes to Complex Traits, Heidelberg, Germany.
  • Int'l Joint Research
• [Presentation] Identification of non-venom protein genes highly expressed in the venom gland of habu (Protobothrops flavoviridis) and their potential contribution to the quality control of venom proteins. (2019)
  • Author(s): Isomoto A, Hisata K, Inoue J, Shoguchi E, Satoh N, Ogawa T, Shibata H.
  • Organizer: 20th World Congress of the International Society of Toxinology, Buenos Aires, Argentina.
  • Int'l Joint Research
• [Presentation] Whole genome sequencing of a Japanese endemic pit viper, habu, Protobothrops flavoviridis reveals accelerated evolution of venom protein genes enriched in microchromosomal regions. (2019)
  • Author(s): Shibata H.
  • Organizer: Integrative Organismal Biology Symposium: Integrating Structural Biology with ‘Omics in Asia-Pacific’, National Tsing Hua University, Hsinchu, Taiwan.
  • Int'l Joint Research / Invited
• [Presentation] ハブベノミクス研究：多様な毒タンパク質は、どのように生み出されるのか？ (2019)
  • Author(s): 小川智久、上田直子、千々岩崇仁、佐藤矩行、柴田弘紀
  • Organizer: 第42回日本分子生物学会年会、福岡国際会議場、福岡
• [Presentation] ホンハブのSSP遺伝子アレイの決定と獲得過程 (2019)
  • Author(s): 稲丸賢人、竹内亜美、前田真理恵、柴田弘紀、服巻保幸、上田直子、服部正策、大野素徳、千々岩崇仁
  • Organizer: 第42回日本分子生物学会年会、福岡国際会議場、福岡
• [Presentation] ホンハブのSSP遺伝子アレイの決定と獲得過程 (2019)
  • Author(s): 稲丸賢人、竹内亜美、前田真理恵、柴田弘紀、服巻保幸、上田直子、服部正策、大野素徳、千々岩崇仁
  • Organizer: 日本爬虫両棲類学会第58回大会、岡山理科大学、岡山
• [Presentation] Whole genome sequencing of a Japanese endemic pit viper, habu, Protobothrops flavoviridis reveals accelerated evolution of venom protein genes enriched in microchromosomal regions. (2018)
  • Author(s): Shibata H, Chijiwa T, Oda-Ueda N, Yamaguchi K, Hattori S, Matsubara K, Matsuda Y, Isomoto A, Koyanagi R, Hisata K, Fukumaki Y, Ohno M, Shoguchi E, Satoh N, Ogawa
  • Organizer: The International Society of Toxinology 2018 European Section Congress, Yerevan, Armenia.
  • Int'l Joint Research
• [Presentation] ホンハブのSmall Serum Protein (SSP)遺伝子アレイの特異な構造と進化 (2018)
  • Author(s): 稲丸賢人、千々岩崇仁、竹内亜美、前田真理恵、山口和晃、柴田弘紀、服部正策、上田直子、大野素徳
  • Organizer: 第41回日本分子生物学会年会、パシフィコ横浜
• [Presentation] Whole genome sequencing of a Japanese endemic pit viper, habu, Protobothrops flavoviridis reveals accelerated evolution of venom protein genes enriched in microchromosomal regions. (2018)
  • Author(s): Shibata H, Chijiwa T, Oda-Ueda N, Yamaguchi K, Hattori S, Matsubara K, Matsuda Y, Koyanagi R, Hisata K, Fukumaki Y, Ohno M, Shoguchi E, Satoh N, Ogawa T.
  • Organizer: SMBE 2018, Yokohama, Japan
  • Int'l Joint Research
• [Presentation] ハブ（Protobothrops flavoviridis）の全ゲノム配列決定から明らかになった毒液関連遺伝子群の多重化および加速進化と染色体構造との関係 (2018)
  • Author(s): 柴田弘紀、千々岩崇仁、小田-上田直子、服部正策、松原和純、松田洋一、山崎慎一、藤江学、後藤大輝、小柳亮、竹内猛、服巻保幸、大野素徳、将口栄一、久田香奈子、佐藤矩行、小川智久
  • Organizer: 日本爬虫両棲類学会第57回大会、麻布大学、相模原
• [Book] 毒ヘビ全書 (2020)
  • Author(s): 田原 義太慶、柴田 弘紀、友永 達也
  • Total Pages: 336
  • Publisher: グラフィック社
  • ISBN: 9784766133134
• [Book] Biomineralization: From Molecular and Nano-structural Analyses to Environmental Science. (2018)
  • Author(s): Ogawa T, Sekikawa A, Sato H, Muramoto K, Shibata H, Hattori S.
  • Total Pages: 413
  • Publisher: Springer Nature, Singapore
  • ISBN: 9789811310010