From the depths of the Java Trench: genomic analysis of Priestia flexa JT4 reveals bioprospecting and lycopene production potential
Abstract Background The marine environment boasts distinctive physical, chemical, and biological characteristics. While numerous studies have delved into the microbial ecology and biological potential of the marine environment, exploration of genetically encoded, deep-sea sourced secondary metabolit...
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2024-12-01
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| author | Ocky K. Radjasa Ray Steven Yosua Natanael Husna Nugrahapraja Septhy K. Radjasa Tati Kristianti Maelita R. Moeis Joko P. Trinugroho Haekal B. Suharya Alfito O. Rachmatsyah Ari Dwijayanti Mutiara R. Putri Charlie E. de Fretes Zen L. Siallagan Muhammad Fadli Rafidha D. A. Opier Jandinta D. Farahyah Viana Rahmawati Meirifa Rizanti Zalfa Humaira Ary S. Prihatmanto Nugroho D. Hananto R. Dwi Susanto Agus Chahyadi Elfahmi Neil Priharto Kamarisima Fenny M. Dwivany |
| author_facet | Ocky K. Radjasa Ray Steven Yosua Natanael Husna Nugrahapraja Septhy K. Radjasa Tati Kristianti Maelita R. Moeis Joko P. Trinugroho Haekal B. Suharya Alfito O. Rachmatsyah Ari Dwijayanti Mutiara R. Putri Charlie E. de Fretes Zen L. Siallagan Muhammad Fadli Rafidha D. A. Opier Jandinta D. Farahyah Viana Rahmawati Meirifa Rizanti Zalfa Humaira Ary S. Prihatmanto Nugroho D. Hananto R. Dwi Susanto Agus Chahyadi Elfahmi Neil Priharto Kamarisima Fenny M. Dwivany |
| author_sort | Ocky K. Radjasa |
| collection | DOAJ |
| description | Abstract Background The marine environment boasts distinctive physical, chemical, and biological characteristics. While numerous studies have delved into the microbial ecology and biological potential of the marine environment, exploration of genetically encoded, deep-sea sourced secondary metabolites remains scarce. This study endeavors to investigate marine bioproducts derived from deep-sea water samples at a depth of 1,000 m in the Java Trench, Indonesia, utilizing both culture-dependent and whole-genome sequencing methods. Results Our efforts led to the successful isolation and cultivation of a bacterium Priestia flexa JT4 from the water samples, followed by comprehensive genome sequencing. The resultant high-quality draft genome, approximately 4 Mb, harbored 5185 coding sequences (CDSs). Notably, 61.97% of these CDSs were inadequately characterized, presenting potential novel CDSs. This study is the first to identify the "open-type" (α < 1) pangenome within the genus Priestia. Moreover, our analysis uncovered eight biosynthetic gene clusters (BGCs) using the common genome mining pipeline, antiSMASH. Two non-ribosomal peptide synthetase (NRPS) BGCs within these clusters exhibited the potential to generate novel biological compounds. Noteworthy is the confirmation that the terpene BGC in P. flexa JT4 can produce lycopene, a compound in substantial industrial demand. The presence of lycopene in the P. flexa JT4 cells was verified using Ultra-performance liquid chromatography-mass spectrometry (UPLC-MS/MS) in multiple reaction modes. Conclusions This study highlights the bioprospecting opportunity to explore novel bioproducts and lycopene compounds from P. flexa JT4. It marks the pioneering exploration of deep-sea bacterium bioprospecting in Indonesia, seeking to unveil novel bioproducts and lycopene compounds through a genome mining approach. |
| format | Article |
| id | doaj-art-64bced756f59470ab7479cbfdab1b5bd |
| institution | Kabale University |
| issn | 1471-2164 |
| language | English |
| publishDate | 2024-12-01 |
| publisher | BMC |
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| series | BMC Genomics |
| spelling | doaj-art-64bced756f59470ab7479cbfdab1b5bd2025-01-05T12:09:32ZengBMCBMC Genomics1471-21642024-12-0125111810.1186/s12864-024-11115-2From the depths of the Java Trench: genomic analysis of Priestia flexa JT4 reveals bioprospecting and lycopene production potentialOcky K. Radjasa0Ray Steven1Yosua Natanael2Husna Nugrahapraja3Septhy K. Radjasa4Tati Kristianti5Maelita R. Moeis6Joko P. Trinugroho7Haekal B. Suharya8Alfito O. Rachmatsyah9Ari Dwijayanti10Mutiara R. Putri11Charlie E. de Fretes12Zen L. Siallagan13Muhammad Fadli14Rafidha D. A. Opier15Jandinta D. Farahyah16Viana Rahmawati17Meirifa Rizanti18Zalfa Humaira19Ary S. Prihatmanto20Nugroho D. Hananto21R. Dwi Susanto22Agus Chahyadi23Elfahmi24Neil Priharto25Kamarisima26Fenny M. Dwivany27Research Center for Deep Sea, The Earth Sciences and Maritime Research Organization, National Research and Innovation AgencyInstitut Teknologi Bandung, School of Life Sciences and TechnologyInstitut Teknologi Bandung, School of Life Sciences and TechnologyInstitut Teknologi Bandung, School of Life Sciences and TechnologyInstitut Teknologi Bandung, School of Life Sciences and TechnologyInstitut Pendidikan IndonesiaDepartment of Biotechnology, Faculty of Science and Technology, Universitas Muhammadiyah BandungResearch Center for Genetic Engineering, Research Organization for Life Science and Environment, National Research and Innovation AgencyInstitut Teknologi Bandung, School of Life Sciences and TechnologyInstitut Teknologi Bandung, School of Life Sciences and TechnologyIndonesia Biogeography and Biodiversity Research InstituteDepartment of Oceanography, Faculty of Earth Science and Technology, Institut Teknologi BandungResearch Center for Deep Sea, The Earth Sciences and Maritime Research Organization, National Research and Innovation AgencyResearch Center for Deep Sea, The Earth Sciences and Maritime Research Organization, National Research and Innovation AgencyResearch Center for Deep Sea, The Earth Sciences and Maritime Research Organization, National Research and Innovation AgencyResearch Center for Deep Sea, The Earth Sciences and Maritime Research Organization, National Research and Innovation AgencyInstitut Teknologi Bandung, School of Life Sciences and TechnologyInstitut Teknologi Bandung, School of Life Sciences and TechnologyInstitut Teknologi Bandung, School of Life Sciences and TechnologyKorean Collection for Type Cultures (KCTC), Biological Resource Center, Korea Research, Institute of Bioscience & Biotechnology (KRIBB)Institut Teknologi Bandung Research Center On Information and Communication TechnologyDirectorate of Research Vessel Management, National Research, and Innovation AgencyDepartment of Atmospheric and Oceanic Science, University of MarylandBioscience and Biotechnology Research Center, Bandung Institute of TechnologyBioscience and Biotechnology Research Center, Bandung Institute of TechnologyInstitut Teknologi Bandung, School of Life Sciences and TechnologyInstitut Teknologi Bandung, School of Life Sciences and TechnologyInstitut Teknologi Bandung, School of Life Sciences and TechnologyAbstract Background The marine environment boasts distinctive physical, chemical, and biological characteristics. While numerous studies have delved into the microbial ecology and biological potential of the marine environment, exploration of genetically encoded, deep-sea sourced secondary metabolites remains scarce. This study endeavors to investigate marine bioproducts derived from deep-sea water samples at a depth of 1,000 m in the Java Trench, Indonesia, utilizing both culture-dependent and whole-genome sequencing methods. Results Our efforts led to the successful isolation and cultivation of a bacterium Priestia flexa JT4 from the water samples, followed by comprehensive genome sequencing. The resultant high-quality draft genome, approximately 4 Mb, harbored 5185 coding sequences (CDSs). Notably, 61.97% of these CDSs were inadequately characterized, presenting potential novel CDSs. This study is the first to identify the "open-type" (α < 1) pangenome within the genus Priestia. Moreover, our analysis uncovered eight biosynthetic gene clusters (BGCs) using the common genome mining pipeline, antiSMASH. Two non-ribosomal peptide synthetase (NRPS) BGCs within these clusters exhibited the potential to generate novel biological compounds. Noteworthy is the confirmation that the terpene BGC in P. flexa JT4 can produce lycopene, a compound in substantial industrial demand. The presence of lycopene in the P. flexa JT4 cells was verified using Ultra-performance liquid chromatography-mass spectrometry (UPLC-MS/MS) in multiple reaction modes. Conclusions This study highlights the bioprospecting opportunity to explore novel bioproducts and lycopene compounds from P. flexa JT4. It marks the pioneering exploration of deep-sea bacterium bioprospecting in Indonesia, seeking to unveil novel bioproducts and lycopene compounds through a genome mining approach.https://doi.org/10.1186/s12864-024-11115-2Deep-sea watersJava TrenchWhole genome sequencingPriestia flexaBiosynthetic gene clusterBioprospecting |
| spellingShingle | Ocky K. Radjasa Ray Steven Yosua Natanael Husna Nugrahapraja Septhy K. Radjasa Tati Kristianti Maelita R. Moeis Joko P. Trinugroho Haekal B. Suharya Alfito O. Rachmatsyah Ari Dwijayanti Mutiara R. Putri Charlie E. de Fretes Zen L. Siallagan Muhammad Fadli Rafidha D. A. Opier Jandinta D. Farahyah Viana Rahmawati Meirifa Rizanti Zalfa Humaira Ary S. Prihatmanto Nugroho D. Hananto R. Dwi Susanto Agus Chahyadi Elfahmi Neil Priharto Kamarisima Fenny M. Dwivany From the depths of the Java Trench: genomic analysis of Priestia flexa JT4 reveals bioprospecting and lycopene production potential BMC Genomics Deep-sea waters Java Trench Whole genome sequencing Priestia flexa Biosynthetic gene cluster Bioprospecting |
| title | From the depths of the Java Trench: genomic analysis of Priestia flexa JT4 reveals bioprospecting and lycopene production potential |
| title_full | From the depths of the Java Trench: genomic analysis of Priestia flexa JT4 reveals bioprospecting and lycopene production potential |
| title_fullStr | From the depths of the Java Trench: genomic analysis of Priestia flexa JT4 reveals bioprospecting and lycopene production potential |
| title_full_unstemmed | From the depths of the Java Trench: genomic analysis of Priestia flexa JT4 reveals bioprospecting and lycopene production potential |
| title_short | From the depths of the Java Trench: genomic analysis of Priestia flexa JT4 reveals bioprospecting and lycopene production potential |
| title_sort | from the depths of the java trench genomic analysis of priestia flexa jt4 reveals bioprospecting and lycopene production potential |
| topic | Deep-sea waters Java Trench Whole genome sequencing Priestia flexa Biosynthetic gene cluster Bioprospecting |
| url | https://doi.org/10.1186/s12864-024-11115-2 |
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