Phylogenomic Identification of a Highly Conserved Copper-Binding RiPP Biosynthetic Gene Cluster in Marine Microbulbifer Bacteria

Conserved biosynthetic gene clusters (BGCs) are often tied to the production of natural products that perform critical functions in an organism’s physiology and ecological interactions. Here, by phylogenetic analysis across the bacterial genus, we report the obligate conservation of a BGC in genomes...

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Main Author:	Yifan Tang (1269402) (author)
Other Authors:	Weimao Zhong (5519135) (author), Longping Fu (11727875) (author), Emmanuel Asante (22277327) (author), Anastasiia Kostenko (6939998) (author), F. N. U. Vidya (19935264) (author), Paige Mandelare-Ruiz (12041634) (author), Tamilore T. Adeogun (22277330) (author), Gabriel P. Anderson (22277333) (author), Benjamin E. Edmonds (22277336) (author), Oscar Fang (22277339) (author), Michelle Han (1618693) (author), Alia S. Hollingsworth (22277342) (author), Amna R. Ingham (22277345) (author), Carlyn R. Kirby (22277348) (author), Alice Landrum (22277351) (author), Connor R. Mack (22277354) (author), Nikki S. Nobari (22277357) (author), Emma J. Oswald (22277360) (author), Cecilia L. Polevoy (22277363) (author), Yasmin Sharifian (22277366) (author), Timothy J. So (22277369) (author), Joelee R. Stokes (22277372) (author), Reniya S. Thompson (22277375) (author), Rishabh Vuthamaraju (22277378) (author), Elaine C. Wang (22277381) (author), William H. Yang (4405492) (author), Alison E. Onstine (22277384) (author), Valerie J. Paul (307783) (author), Ronghu Wu (1643710) (author), Allegra T. Aron (14607873) (author), Vinayak Agarwal (1335897) (author)
Published:	2025
Subjects:	Biochemistry Microbiology Genetics Evolutionary Biology Ecology Inorganic Chemistry Environmental Sciences not elsewhere classified Biological Sciences not elsewhere classified structure elucidated using perform critical functions nmr spectroscopy  natural product chemistry phylogenetic analysis across microbulbifer genomes regardless highly conserved copper natural products copper chelator undergraduate students provide hands phylogenomic identification pedagogic setting organism ’ often tied obligate conservation mass spectrometry georgia institute geographical dispersal genome mining ecological interactions common member bgc  bacterial phylogeny
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author	Yifan Tang (1269402)
author2	Weimao Zhong (5519135) Longping Fu (11727875) Emmanuel Asante (22277327) Anastasiia Kostenko (6939998) F. N. U. Vidya (19935264) Paige Mandelare-Ruiz (12041634) Tamilore T. Adeogun (22277330) Gabriel P. Anderson (22277333) Benjamin E. Edmonds (22277336) Oscar Fang (22277339) Michelle Han (1618693) Alia S. Hollingsworth (22277342) Amna R. Ingham (22277345) Carlyn R. Kirby (22277348) Alice Landrum (22277351) Connor R. Mack (22277354) Nikki S. Nobari (22277357) Emma J. Oswald (22277360) Cecilia L. Polevoy (22277363) Yasmin Sharifian (22277366) Timothy J. So (22277369) Joelee R. Stokes (22277372) Reniya S. Thompson (22277375) Rishabh Vuthamaraju (22277378) Elaine C. Wang (22277381) William H. Yang (4405492) Alison E. Onstine (22277384) Valerie J. Paul (307783) Ronghu Wu (1643710) Allegra T. Aron (14607873) Vinayak Agarwal (1335897)
author2_role	author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author
author_facet	Yifan Tang (1269402) Weimao Zhong (5519135) Longping Fu (11727875) Emmanuel Asante (22277327) Anastasiia Kostenko (6939998) F. N. U. Vidya (19935264) Paige Mandelare-Ruiz (12041634) Tamilore T. Adeogun (22277330) Gabriel P. Anderson (22277333) Benjamin E. Edmonds (22277336) Oscar Fang (22277339) Michelle Han (1618693) Alia S. Hollingsworth (22277342) Amna R. Ingham (22277345) Carlyn R. Kirby (22277348) Alice Landrum (22277351) Connor R. Mack (22277354) Nikki S. Nobari (22277357) Emma J. Oswald (22277360) Cecilia L. Polevoy (22277363) Yasmin Sharifian (22277366) Timothy J. So (22277369) Joelee R. Stokes (22277372) Reniya S. Thompson (22277375) Rishabh Vuthamaraju (22277378) Elaine C. Wang (22277381) William H. Yang (4405492) Alison E. Onstine (22277384) Valerie J. Paul (307783) Ronghu Wu (1643710) Allegra T. Aron (14607873) Vinayak Agarwal (1335897)
author_role	author
dc.creator.none.fl_str_mv	Yifan Tang (1269402) Weimao Zhong (5519135) Longping Fu (11727875) Emmanuel Asante (22277327) Anastasiia Kostenko (6939998) F. N. U. Vidya (19935264) Paige Mandelare-Ruiz (12041634) Tamilore T. Adeogun (22277330) Gabriel P. Anderson (22277333) Benjamin E. Edmonds (22277336) Oscar Fang (22277339) Michelle Han (1618693) Alia S. Hollingsworth (22277342) Amna R. Ingham (22277345) Carlyn R. Kirby (22277348) Alice Landrum (22277351) Connor R. Mack (22277354) Nikki S. Nobari (22277357) Emma J. Oswald (22277360) Cecilia L. Polevoy (22277363) Yasmin Sharifian (22277366) Timothy J. So (22277369) Joelee R. Stokes (22277372) Reniya S. Thompson (22277375) Rishabh Vuthamaraju (22277378) Elaine C. Wang (22277381) William H. Yang (4405492) Alison E. Onstine (22277384) Valerie J. Paul (307783) Ronghu Wu (1643710) Allegra T. Aron (14607873) Vinayak Agarwal (1335897)
dc.date.none.fl_str_mv	2025-09-19T15:07:23Z
dc.identifier.none.fl_str_mv	10.1021/acschembio.5c00507.s002
dc.relation.none.fl_str_mv	https://figshare.com/articles/dataset/Phylogenomic_Identification_of_a_Highly_Conserved_Copper-Binding_RiPP_Biosynthetic_Gene_Cluster_in_Marine_Microbulbifer_Bacteria/30166124
dc.rights.none.fl_str_mv	CC BY-NC 4.0 info:eu-repo/semantics/openAccess
dc.subject.none.fl_str_mv	Biochemistry Microbiology Genetics Evolutionary Biology Ecology Inorganic Chemistry Environmental Sciences not elsewhere classified Biological Sciences not elsewhere classified structure elucidated using perform critical functions nmr spectroscopy  natural product chemistry phylogenetic analysis across microbulbifer genomes regardless highly conserved copper natural products copper chelator undergraduate students provide hands phylogenomic identification pedagogic setting organism ’ often tied obligate conservation mass spectrometry georgia institute geographical dispersal genome mining ecological interactions common member bgc  bacterial phylogeny
dc.title.none.fl_str_mv	Phylogenomic Identification of a Highly Conserved Copper-Binding RiPP Biosynthetic Gene Cluster in Marine Microbulbifer Bacteria
dc.type.none.fl_str_mv	Dataset info:eu-repo/semantics/publishedVersion dataset
description	Conserved biosynthetic gene clusters (BGCs) are often tied to the production of natural products that perform critical functions in an organism’s physiology and ecological interactions. Here, by phylogenetic analysis across the bacterial genus, we report the obligate conservation of a BGC in genomes of cosmopolitan marine Microbulbifer bacteria. This genus is a common member of marine microbiomes, and this BGC was conserved in Microbulbifer genomes regardless of phylogenetic or geographical dispersal. The post-translationally modified peptidic product encoded by this BGCwhich was accessed via heterologous production and its structure elucidated using a combination of mass spectrometry and NMR spectroscopywas found to be a copper chelator. Similar BGCs were then found in genomes of other marine bacterial genera coinhabiting the microbiomes of sponges and corals. The phylogenomic workflows described herein were implemented in a pedagogic setting at the Georgia Institute of Technology to provide hands-on instruction to undergraduate students in bacterial phylogeny, genome mining, and natural product chemistry.
eu_rights_str_mv	openAccess
id	Manara_4bf5eac2fb80eae05fcc6d799cd9bc44
identifier_str_mv	10.1021/acschembio.5c00507.s002
network_acronym_str	Manara
network_name_str	ManaraRepo
oai_identifier_str	oai:figshare.com:article/30166124
publishDate	2025
repository.mail.fl_str_mv
repository.name.fl_str_mv
repository_id_str
rights_invalid_str_mv	CC BY-NC 4.0
spelling	Phylogenomic Identification of a Highly Conserved Copper-Binding RiPP Biosynthetic Gene Cluster in Marine Microbulbifer BacteriaYifan Tang (1269402)Weimao Zhong (5519135)Longping Fu (11727875)Emmanuel Asante (22277327)Anastasiia Kostenko (6939998)F. N. U. Vidya (19935264)Paige Mandelare-Ruiz (12041634)Tamilore T. Adeogun (22277330)Gabriel P. Anderson (22277333)Benjamin E. Edmonds (22277336)Oscar Fang (22277339)Michelle Han (1618693)Alia S. Hollingsworth (22277342)Amna R. Ingham (22277345)Carlyn R. Kirby (22277348)Alice Landrum (22277351)Connor R. Mack (22277354)Nikki S. Nobari (22277357)Emma J. Oswald (22277360)Cecilia L. Polevoy (22277363)Yasmin Sharifian (22277366)Timothy J. So (22277369)Joelee R. Stokes (22277372)Reniya S. Thompson (22277375)Rishabh Vuthamaraju (22277378)Elaine C. Wang (22277381)William H. Yang (4405492)Alison E. Onstine (22277384)Valerie J. Paul (307783)Ronghu Wu (1643710)Allegra T. Aron (14607873)Vinayak Agarwal (1335897)BiochemistryMicrobiologyGeneticsEvolutionary BiologyEcologyInorganic ChemistryEnvironmental Sciences not elsewhere classifiedBiological Sciences not elsewhere classifiedstructure elucidated usingperform critical functionsnmr spectroscopy natural product chemistryphylogenetic analysis acrossmicrobulbifer genomes regardlesshighly conserved coppernatural productscopper chelatorundergraduate studentsprovide handsphylogenomic identificationpedagogic settingorganism ’often tiedobligate conservationmass spectrometrygeorgia institutegeographical dispersalgenome miningecological interactionscommon memberbgc bacterial phylogenyConserved biosynthetic gene clusters (BGCs) are often tied to the production of natural products that perform critical functions in an organism’s physiology and ecological interactions. Here, by phylogenetic analysis across the bacterial genus, we report the obligate conservation of a BGC in genomes of cosmopolitan marine Microbulbifer bacteria. This genus is a common member of marine microbiomes, and this BGC was conserved in Microbulbifer genomes regardless of phylogenetic or geographical dispersal. The post-translationally modified peptidic product encoded by this BGCwhich was accessed via heterologous production and its structure elucidated using a combination of mass spectrometry and NMR spectroscopywas found to be a copper chelator. Similar BGCs were then found in genomes of other marine bacterial genera coinhabiting the microbiomes of sponges and corals. The phylogenomic workflows described herein were implemented in a pedagogic setting at the Georgia Institute of Technology to provide hands-on instruction to undergraduate students in bacterial phylogeny, genome mining, and natural product chemistry.2025-09-19T15:07:23ZDatasetinfo:eu-repo/semantics/publishedVersiondataset10.1021/acschembio.5c00507.s002https://figshare.com/articles/dataset/Phylogenomic_Identification_of_a_Highly_Conserved_Copper-Binding_RiPP_Biosynthetic_Gene_Cluster_in_Marine_Microbulbifer_Bacteria/30166124CC BY-NC 4.0info:eu-repo/semantics/openAccessoai:figshare.com:article/301661242025-09-19T15:07:23Z
spellingShingle	Phylogenomic Identification of a Highly Conserved Copper-Binding RiPP Biosynthetic Gene Cluster in Marine Microbulbifer Bacteria Yifan Tang (1269402) Biochemistry Microbiology Genetics Evolutionary Biology Ecology Inorganic Chemistry Environmental Sciences not elsewhere classified Biological Sciences not elsewhere classified structure elucidated using perform critical functions nmr spectroscopy  natural product chemistry phylogenetic analysis across microbulbifer genomes regardless highly conserved copper natural products copper chelator undergraduate students provide hands phylogenomic identification pedagogic setting organism ’ often tied obligate conservation mass spectrometry georgia institute geographical dispersal genome mining ecological interactions common member bgc  bacterial phylogeny
status_str	publishedVersion
title	Phylogenomic Identification of a Highly Conserved Copper-Binding RiPP Biosynthetic Gene Cluster in Marine Microbulbifer Bacteria
title_full	Phylogenomic Identification of a Highly Conserved Copper-Binding RiPP Biosynthetic Gene Cluster in Marine Microbulbifer Bacteria
title_fullStr	Phylogenomic Identification of a Highly Conserved Copper-Binding RiPP Biosynthetic Gene Cluster in Marine Microbulbifer Bacteria
title_full_unstemmed	Phylogenomic Identification of a Highly Conserved Copper-Binding RiPP Biosynthetic Gene Cluster in Marine Microbulbifer Bacteria
title_short	Phylogenomic Identification of a Highly Conserved Copper-Binding RiPP Biosynthetic Gene Cluster in Marine Microbulbifer Bacteria
title_sort	Phylogenomic Identification of a Highly Conserved Copper-Binding RiPP Biosynthetic Gene Cluster in Marine Microbulbifer Bacteria
topic	Biochemistry Microbiology Genetics Evolutionary Biology Ecology Inorganic Chemistry Environmental Sciences not elsewhere classified Biological Sciences not elsewhere classified structure elucidated using perform critical functions nmr spectroscopy  natural product chemistry phylogenetic analysis across microbulbifer genomes regardless highly conserved copper natural products copper chelator undergraduate students provide hands phylogenomic identification pedagogic setting organism ’ often tied obligate conservation mass spectrometry georgia institute geographical dispersal genome mining ecological interactions common member bgc  bacterial phylogeny

Phylogenomic Identification of a Highly Conserved Copper-Binding RiPP Biosynthetic Gene Cluster in Marine Microbulbifer Bacteria

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