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Nurul Khumaida
Departemen Agronomi Dan Hortikultura, Fakultas Pertanian, Institut Pertanian Bogor (Bogor Agricultural University), Jl. Meranti Kampus IPB Darmaga, Bogor 16680, Indonesia
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Journal : Menara Perkebunan

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Identifikasi famili gen putatif penyandi protease inhibitor dengan pendekatan in silico komparatif pada genom Hevea brasiliensis Muell. Arg (Identification of putative gene family encoding protease inhibitors by in silico comparative analysis in Hevea brasiliensis Muell. Arg genome) Irfan MARTIANSYAH; Riza Arief PUTRANTO; Nurul KHUMAIDA
E-Journal Menara Perkebunan Vol 85, No 2 (2017): Oktober 2017
Publisher : INDONESIAN RESEARCH INSTITUTE FOR BIOTECHNOLOGY AND BIOINDUSTRY

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (807.039 KB) | DOI: 10.22302/iribb.jur.mp.v85i2.257

Abstract

AbstractProtease inhibitors (PIs) are small proteins that form complexes with proteases and inhibits their proteolytic activity. Its potential application as an antimicrobial agent has been studied. Most of PIs' molecule size is around 8-22 kDa depending on their protein families.To date, on the basis of sequence homologies of inhibitor domains, PIs have been classified into 48 families in all organisms. In plant, more than 13 families of PIs have been identified but they were not widely identified in the rubber tree (Hevea brasiliensis Muell.Arg). In the present study, 40 putative HbPI genes, designated as HbPI01 to HbPI36, were identified from whole-genome sequence of rubber tree clone Reyan 7-33-97 using 7453 scaffolds available online in NCBI with the accession code: LVXX01000000. Multiple sequence alignment using MUSCLE algorithm discovered seven conserved motifs (Motifs I-VII) among HbPIs. Phylogenetic analysis of 50 and 36 PI amino acid residues of 32 scaffolds containing putative PI genes from Arabidopsis thaliana and H. brasiliensis showed three clusters (families): LTP-I, SERPIN and LTP-II. LTP-I has 23 putative HbPI genes (HbPI05 to HbPI27) and 12 AtPI genes. SERPIN, a family member of serine protease inhibitor group, has 11 putative HbPI genes (HbPI01 to HbPI04 and HbPI28 to HbPI34) and 22 AtPI genes. LTP-II has 2 putative HbPI genes (HbPI35 to HbPI36) and 16 AtPI genes. In conclusion, this work provides valuable information for further functional characterization of HbPI genes in H. brasiliensis.[Key words: protease inhibitor, genome-wide, scaffold, in silico, Hevea brasiliensis]. AbstrakProtease inhibitor (PI) merupakan protein yang membentuk kompleks dengan protease dan menghambat aktivitas proteolitik dari enzim tersebut. Potensi penggunaan protease inhibitor sebagai agensia antimikroba telah diketahui. Kebanyakan PI memiliki ukuran molekul sekitar 8-22 kDa bergantung pada familinya. Saat ini, PI dapat diklasifikasikan menjadi 48 famili di seluruh organisme berdasarkan kemiripan sekuen dari domain inhibitornya. Pada tanaman, lebih dari 13 famili PI telah diketahui tetapi pada tanaman karet (Hevea brasiliensis Muell.Arg) belum diidentifikasi. Pada penelitian ini, sebanyak 40 gen putatif penyandi PI (HbPI01 hingga HbPI36) telah berhasil diidentifikasi dari 7453 scaffold genom utuh tanaman karet klon Reyan 7-33-97 yang tersedia secara daring dengan kode aksesi LVXX01000000. Penjajaran sekuen menggunakan algoritma MUSCLE memper-lihatkan tujuh konservasi motif (Motif I-VIII) pada famili gen putatif HbPIs. Analisis pohon filogenetik dari tanaman Arabidopsis thaliana dan H. brasiliensis sebanyak 50 dan 36 sekuen residu asam amino dari 32 scaffold yang mengandung gen putatif PI menunjukkan adanya tiga klaster besar, yaitu famili LTP-I, SERPIN dan LTP-II. LTP-I terdiri dari 23 gen putatif HbPI (HbPI05 hingga HbPI27) dan 12 gen AtPI. SERPIN yang merupakan anggota kelas protease inhibitor serin terdiri dari 11 gen putatif HbPI (HbPI01hingga HbPI04 dan HbPI28 hingga HbPI34) dan 22 gen AtPI. LTP-II terdiri dari 2 gen putatif HbPI (HbPI35 hingga HbPI36) dan 16 gen AtPIs. Penelitian ini menghasilkan informasi penting untuk melakukan karakterisasi fungsional lebih mendalam pada gen HbPI tanaman karet ke depannya.[Kata kunci: protease inhibitor, genome-wide,scaffold, in silico, Hevea brasiliensis].
Co-Authors , Kisman , Sukendah , Witjaksono . Wusnah A. Sofwan Achmad . ADI SETIADI Agus Purwito Agustina, Ferra Anggita AHMAD JUNAEDI Ahmad Rifqi Fauzi Ali Djamhuri Almia Permata Putri Amril Aman Andi Dahliaty Aniversari Apriana Aniversari Apriana Aniversari Apriana Ardana, I. N. Kutha Ardie, and Sintho Wahyuning Ardie, dan Sintho Wahyuning Aris Purwanto Arrin Rosmala Atmitri Sisharmini Atmitri Sisharmini Atmitri Sisharmini Bambang S. Purwoko Bambang Sapta Purwoko Bhayu Hartanti Bintang, dan Maria Buang Abdullah Cakranegara, Pandu Adi Cucu Sukmana, Cucu Danar Dono Dede J Sudrajat Dede J. Sudrajat Dede J. Sudrajat Dede J. Sudrajat Dede Jajat Sudrajat Dede Kurniadi DEWI SARTIAMI Dewi Sukma Dewi Sukma Didy Sopandie Diny Dinarti Dwi Pratiwi Edi Santosa Efendi, Darda Emmy Darmawati Enny Sudarmonowati Evi Fitriany Faqih Udin Firdausya, Andina Fabrini Freddy Tua Musa Panggabean Gustaaf A Wattimena, Gustaaf A Gustaaf A. Wattimena Gustaaf Adolf Wattimena Gustaaf Adolf Wattimena HADIPOENTYANTI, ENDANG Hartati, RR. Sri Heldiyanti, Rina Hendri Hermawan Adinugraha HUSNI, ALI I Ismayani I MADE ARTIKA Ida Duma Riris Ika Mariska Ika Mariska Ika Mariska Ika Mariska Ika Mariska Ika Mariska Ika Roostika Ika Roostika Ika Roostika Indrastuti Apri Rumanti Irdika Mansur Irfan MARTIANSYAH Iskandar Z. Siregar ISKANDAR ZULKARNAEN SIREGAR Iswari S Dewi Iswari S. Dewi Iswari Saraswati Dewi Jalaluddin Jalaluddin Kartika Ning Tyas Kartika Ning Tyas Kasutjianingati . Kisman Kisman Kurniawan R. Trijatmiko Kurniawan Rudi Trijatmiko Kurniawan Rudi Trijatmiko La Muhuria Lefin Kafindra Lestari, Risza Putri Lisnawaty Simatupang Lola Adres Yanti Lukman Hakim M Murtadha M. Amir M. Asyabul Zikki Maemonah, Maemonah MARIA BINTANG Marini Damanik Mariska, Ika Maryati Evivani Doloksaribu MEYNARTI SARI DEWI IBRAHIM MEYNARTI SARI DEWI IBRAHIM Muaz Adbdul Karim Muaz Adbdul Karim Muhamad Syukur Muhammad Irfan Habibi MUHAMMAD SYUKUR Mulyatno, Mulyatno Munif Ghulamahdi N. Sri i Hartati Nafilawati wa ode Nata Suharta Natalini Nova Kristina Natalini Nova Kristina Nataniel Tandirogang Nugroho, Candra Catur Nura ,, Nura Nurbaiti Nurbaiti Nurhasybi Nurhasybi Nurul Fatimah Nurul Fauziah O K Sofyan OTIH ROSTIANA OTIH ROSTIANA Pienyani Rosawanti Rahmi Henda Yani Rasyad, M. Ashadi Reny Herawati Rina Hapsari Wening, Rina Hapsari Rinda Cahyana Riyanti Catrina H S Riza Arief PUTRANTO Rizkiannur Putri, Amalia Roedhy Poerwanto Rossa Yunita Rossa Yunita Rossa Yunita Rozanna Dewi Ryan Budi Setiawan Sadewi Maharani Sadewi Maharani, Sadewi Saepudin, Adam Safitri Safitri Saronom S ilaban Sarwono Hardjowigeno Shafwan Fahmi Silawati, Tutisiana Silawati Tutisiana Sintho Wahyuning Ardie Siregar, Ulfah J Siswati, Leni Siti Aisyah Siti Kurniawati Slamet Budijanto Slamet Susanto Sobir Sobir Sri Enny Triwidiastuti Sri Helianty Sry Rahmadani Subekti, Isnani Sudarsono Sudarsono Sudarsono Suhesti, Sri Sukma, Dewi Sulastri Sulastri Sulhatun Sulhatun SUPRIADI SUPRIADI Suryati Suryati Suryo Wiyono Sutalaksana, Iftikar Z Sutrisno Mardjan Sutrisno, Sutrisno Suyanti Kasimin Syamsul Bahri Syamsul Bahri Tarigan, Asmara Iriani Tengku Mia Rahmiati Teti Arabia Thifany, Ariny Jihan Tri Handayani Tri Joko Santoso Tri Lestari Mardiningsih Tri Lestari Mardiningsih, Tri Lestari Trijatmiko, dan Kurniawan Rudi Trikoesoemaningtyas Trismi Ristyowati Ulfah J. Siregar Ulfah Juniarti Siregar Ummu Kalsum Wahyuning Ardie, dan Sintho Waizul Fahri Purba Waras Nurcholis Warid Warid Wattimena, and Gustaaf Adolf WATTIMENA, G. A. Wening Enggarini Wening Enggarini Widiatmaka Widodo , Widowati, Sartika Widya Hartati, Widya Wijayanti, Mustika Eka Willy Bayuardi Suwarno Yudiansyah Yudiansyah Yulia, Endah Yulia Yundari, Yundari Yunita, Rossa Zuli Nuraeni