Genome mining reveals unlocked bioactive potential of marine Gram-negative bacteria

Machado, Henrique; Sonnenschein, Eva C.; Melchiorsen, Jette; Gram, Lone

doi:10.1186/s12864-015-1365-z

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Genome mining reveals unlocked bioactive potential of marine Gram-negative bacteria

Henrique Machado, Eva C. Sonnenschein

, Jette Melchiorsen, Lone Gram

BMC Genomics, Volume: 16, Issue: 1

Swansea University Author: Eva C. Sonnenschein

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DOI (Published version): 10.1186/s12864-015-1365-z

Abstract

BackgroundAntibiotic resistance in bacteria spreads quickly, overtaking the pace at which new compounds are discovered and this emphasizes the immediate need to discover new compounds for control of infectious diseases. Terrestrial bacteria have for decades been investigated as a source of bioactive...

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Published in:	BMC Genomics
ISSN:	1471-2164
Published:	Springer Science and Business Media LLC 2015
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URI:	https://cronfa.swan.ac.uk/Record/cronfa61738
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Marine bacteria have so far not been exploited to the same extent; however, they are believed to harbor a multitude of novel bioactive chemistry. To explore this potential, genomes of 21 marine Alpha- and Gammaproteobacteria collected during the Galathea 3 expedition were sequenced and mined for natural product encoding gene clusters.ResultsIndependently of genome size, bacteria of all tested genera carried a large number of clusters encoding different potential bioactivities, especially within the Vibrionaceae and Pseudoalteromonadaceae families. A very high potential was identified in pigmented pseudoalteromonads with up to 20 clusters in a single strain, mostly NRPSs and NRPS-PKS hybrids. Furthermore, regulatory elements in bioactivity-related pathways including chitin metabolism, quorum sensing and iron scavenging systems were investigated both in silico and in vitro. Genes with siderophore function were identified in 50% of the strains, however, all but one harboured the ferric-uptake-regulator gene. Genes encoding the syntethase of acylated homoserine lactones were found in Roseobacter-clade bacteria, but not in the Vibrionaceae strains and only in one Pseudoalteromonas strains. The understanding and manipulation of these elements can help in the discovery and production of new compounds never identified under regular laboratory cultivation conditions. High chitinolytic potential was demonstrated and verified for Vibrio and Pseudoalteromonas species that commonly live in close association with eukaryotic organisms in the environment. Chitin regulation by the ChiS histidine-kinase seems to be a general trait of the Vibrionaceae family, however it is absent in the Pseudomonadaceae. Hence, the degree to which chitin influences secondary metabolism in marine bacteria is not known.ConclusionsUtilizing the rapidly developing sequencing technologies and software tools in combination with phenotypic in vitro assays, we demonstrated the high bioactive potential of marine bacteria in an efficient, straightforward manner – an approach that will facilitate natural product discovery in the future.</abstract><type>Journal Article</type><journal>BMC Genomics</journal><volume>16</volume><journalNumber>1</journalNumber><paginationStart/><paginationEnd/><publisher>Springer Science and Business Media LLC</publisher><placeOfPublication/><isbnPrint/><isbnElectronic/><issnPrint/><issnElectronic>1471-2164</issnElectronic><keywords>AntiSMASH; Genome mining; Pseudoalteromonas; Secondary metabolites; Vibrionaceae</keywords><publishedDay>7</publishedDay><publishedMonth>3</publishedMonth><publishedYear>2015</publishedYear><publishedDate>2015-03-07</publishedDate><doi>10.1186/s12864-015-1365-z</doi><url/><notes/><college>COLLEGE NANME</college><department>Biosciences</department><CollegeCode>COLLEGE CODE</CollegeCode><DepartmentCode>SBI</DepartmentCode><institution>Swansea University</institution><apcterm/><funders/><projectreference/><lastEdited>2022-11-04T13:52:49.5112833</lastEdited><Created>2022-10-31T15:22:40.6450309</Created><path><level id="1">Faculty of Science and Engineering</level><level id="2">School of Biosciences, Geography and Physics - Biosciences</level></path><authors><author><firstname>Henrique</firstname><surname>Machado</surname><order>1</order></author><author><firstname>Eva C.</firstname><surname>Sonnenschein</surname><orcid>0000-0001-6959-5100</orcid><order>2</order></author><author><firstname>Jette</firstname><surname>Melchiorsen</surname><order>3</order></author><author><firstname>Lone</firstname><surname>Gram</surname><order>4</order></author></authors><documents><document><filename>61738__25652__be6ab64acf694658b57bb916b772a60a.pdf</filename><originalFilename>61738_VoR.pdf</originalFilename><uploaded>2022-11-04T13:52:01.6829818</uploaded><type>Output</type><contentLength>1069432</contentLength><contentType>application/pdf</contentType><version>Version of Record</version><cronfaStatus>true</cronfaStatus><documentNotes>© 2015 Machado et al.; licensee BioMed Central. 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spelling	2022-11-04T13:52:49.5112833 v2 61738 2022-10-31 Genome mining reveals unlocked bioactive potential of marine Gram-negative bacteria f6a4027578a15ea3e6453a54b849c686 0000-0001-6959-5100 Eva C. Sonnenschein Eva C. Sonnenschein true false 2022-10-31 SBI BackgroundAntibiotic resistance in bacteria spreads quickly, overtaking the pace at which new compounds are discovered and this emphasizes the immediate need to discover new compounds for control of infectious diseases. Terrestrial bacteria have for decades been investigated as a source of bioactive compounds leading to successful applications in pharmaceutical and biotech industries. Marine bacteria have so far not been exploited to the same extent; however, they are believed to harbor a multitude of novel bioactive chemistry. To explore this potential, genomes of 21 marine Alpha- and Gammaproteobacteria collected during the Galathea 3 expedition were sequenced and mined for natural product encoding gene clusters.ResultsIndependently of genome size, bacteria of all tested genera carried a large number of clusters encoding different potential bioactivities, especially within the Vibrionaceae and Pseudoalteromonadaceae families. A very high potential was identified in pigmented pseudoalteromonads with up to 20 clusters in a single strain, mostly NRPSs and NRPS-PKS hybrids. Furthermore, regulatory elements in bioactivity-related pathways including chitin metabolism, quorum sensing and iron scavenging systems were investigated both in silico and in vitro. Genes with siderophore function were identified in 50% of the strains, however, all but one harboured the ferric-uptake-regulator gene. Genes encoding the syntethase of acylated homoserine lactones were found in Roseobacter-clade bacteria, but not in the Vibrionaceae strains and only in one Pseudoalteromonas strains. The understanding and manipulation of these elements can help in the discovery and production of new compounds never identified under regular laboratory cultivation conditions. High chitinolytic potential was demonstrated and verified for Vibrio and Pseudoalteromonas species that commonly live in close association with eukaryotic organisms in the environment. Chitin regulation by the ChiS histidine-kinase seems to be a general trait of the Vibrionaceae family, however it is absent in the Pseudomonadaceae. Hence, the degree to which chitin influences secondary metabolism in marine bacteria is not known.ConclusionsUtilizing the rapidly developing sequencing technologies and software tools in combination with phenotypic in vitro assays, we demonstrated the high bioactive potential of marine bacteria in an efficient, straightforward manner – an approach that will facilitate natural product discovery in the future. Journal Article BMC Genomics 16 1 Springer Science and Business Media LLC 1471-2164 AntiSMASH; Genome mining; Pseudoalteromonas; Secondary metabolites; Vibrionaceae 7 3 2015 2015-03-07 10.1186/s12864-015-1365-z COLLEGE NANME Biosciences COLLEGE CODE SBI Swansea University 2022-11-04T13:52:49.5112833 2022-10-31T15:22:40.6450309 Faculty of Science and Engineering School of Biosciences, Geography and Physics - Biosciences Henrique Machado 1 Eva C. Sonnenschein 0000-0001-6959-5100 2 Jette Melchiorsen 3 Lone Gram 4 61738__25652__be6ab64acf694658b57bb916b772a60a.pdf 61738_VoR.pdf 2022-11-04T13:52:01.6829818 Output 1069432 application/pdf Version of Record true © 2015 Machado et al.; licensee BioMed Central. This is an Open Access article distributed under the terms of the Creative Commons Attribution License true eng http://creativecommons.org/licenses/by/4.0
title	Genome mining reveals unlocked bioactive potential of marine Gram-negative bacteria
spellingShingle	Genome mining reveals unlocked bioactive potential of marine Gram-negative bacteria Eva C. Sonnenschein
title_short	Genome mining reveals unlocked bioactive potential of marine Gram-negative bacteria
title_full	Genome mining reveals unlocked bioactive potential of marine Gram-negative bacteria
title_fullStr	Genome mining reveals unlocked bioactive potential of marine Gram-negative bacteria
title_full_unstemmed	Genome mining reveals unlocked bioactive potential of marine Gram-negative bacteria
title_sort	Genome mining reveals unlocked bioactive potential of marine Gram-negative bacteria
author_id_str_mv	f6a4027578a15ea3e6453a54b849c686
author_id_fullname_str_mv	f6a4027578a15ea3e6453a54b849c686_***_Eva C. Sonnenschein
author	Eva C. Sonnenschein
author2	Henrique Machado Eva C. Sonnenschein Jette Melchiorsen Lone Gram
format	Journal article
container_title	BMC Genomics
container_volume	16
container_issue	1
publishDate	2015
institution	Swansea University
issn	1471-2164
doi_str_mv	10.1186/s12864-015-1365-z
publisher	Springer Science and Business Media LLC
college_str	Faculty of Science and Engineering
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hierarchy_top_title	Faculty of Science and Engineering
hierarchy_parent_id	facultyofscienceandengineering
hierarchy_parent_title	Faculty of Science and Engineering
department_str	School of Biosciences, Geography and Physics - Biosciences{{{_:::_}}}Faculty of Science and Engineering{{{_:::_}}}School of Biosciences, Geography and Physics - Biosciences
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description	BackgroundAntibiotic resistance in bacteria spreads quickly, overtaking the pace at which new compounds are discovered and this emphasizes the immediate need to discover new compounds for control of infectious diseases. Terrestrial bacteria have for decades been investigated as a source of bioactive compounds leading to successful applications in pharmaceutical and biotech industries. Marine bacteria have so far not been exploited to the same extent; however, they are believed to harbor a multitude of novel bioactive chemistry. To explore this potential, genomes of 21 marine Alpha- and Gammaproteobacteria collected during the Galathea 3 expedition were sequenced and mined for natural product encoding gene clusters.ResultsIndependently of genome size, bacteria of all tested genera carried a large number of clusters encoding different potential bioactivities, especially within the Vibrionaceae and Pseudoalteromonadaceae families. A very high potential was identified in pigmented pseudoalteromonads with up to 20 clusters in a single strain, mostly NRPSs and NRPS-PKS hybrids. Furthermore, regulatory elements in bioactivity-related pathways including chitin metabolism, quorum sensing and iron scavenging systems were investigated both in silico and in vitro. Genes with siderophore function were identified in 50% of the strains, however, all but one harboured the ferric-uptake-regulator gene. Genes encoding the syntethase of acylated homoserine lactones were found in Roseobacter-clade bacteria, but not in the Vibrionaceae strains and only in one Pseudoalteromonas strains. The understanding and manipulation of these elements can help in the discovery and production of new compounds never identified under regular laboratory cultivation conditions. High chitinolytic potential was demonstrated and verified for Vibrio and Pseudoalteromonas species that commonly live in close association with eukaryotic organisms in the environment. Chitin regulation by the ChiS histidine-kinase seems to be a general trait of the Vibrionaceae family, however it is absent in the Pseudomonadaceae. Hence, the degree to which chitin influences secondary metabolism in marine bacteria is not known.ConclusionsUtilizing the rapidly developing sequencing technologies and software tools in combination with phenotypic in vitro assays, we demonstrated the high bioactive potential of marine bacteria in an efficient, straightforward manner – an approach that will facilitate natural product discovery in the future.
published_date	2015-03-07T04:20:47Z
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Genome mining reveals unlocked bioactive potential of marine Gram-negative bacteria

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