A metabologenomics approach to unlock the metabolome of the novel Antarctic deep-sea isolate Lacinutrix shetlandiensis sp. nov. WUR7

Giovanni A Vitale; Grant G January; Ernest Oppong-Danquah; Gerardo Della Sala; Fortunato Palma Esposito; Deniz Tasdemir; Donatella de Pascale

doi:10.1093/pnasnexus/pgad221

A metabologenomics approach to unlock the metabolome of the novel Antarctic deep-sea isolate Lacinutrix shetlandiensis sp. nov. WUR7

PNAS Nexus. 2023 Jul 6;2(7):pgad221. doi: 10.1093/pnasnexus/pgad221. eCollection 2023 Jul.

Authors

Giovanni A Vitale^{1

2

3}, Grant G January^{4

3}, Ernest Oppong-Danquah⁵, Gerardo Della Sala², Fortunato Palma Esposito^{2

3}, Deniz Tasdemir^{5

6}, Donatella de Pascale^{2

3}

Affiliations

¹ CMFI Cluster of Excellence, Interfaculty Institute of Microbiology and Medicine, University of Tübingen, Tübingen 72076, Germany.
² Department of Ecosustainable Marine Biotechnology, Stazione Zoologica Anton Dohrn, Giardini Molosiglio, Via F.A. Acton 55, 80133, Naples, Italy.
³ Institute of Biochemistry and Cell Biology (IBBC), National Research Council, Via Pietro Castellino 111, 80131 Naples, Italy.
⁴ Derriford Research Facility, School of Biomedical Sciences, Faculty of Health, University of Plymouth, 14 Research Way, Plymouth PL6 8BU, UK.
⁵ GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Am Kiel-Kanal 44, Kiel 24106, Germany.
⁶ Kiel University, Christian-Albrechts-Platz 4, Kiel 24118, Germany.

Abstract

The South Shetland Trough, Antarctica, is an underexplored region for microbiological and biotechnological exploitation. Herein, we describe the isolation and characterization of the novel bacterium Lacinutrix shetlandiensis sp. nov. WUR7 from a deep-sea environment. We explored its chemical diversity via a metabologenomics approach, wherein the OSMAC strategy was strategically employed to upregulate cryptic genes for secondary metabolite production. Based on hybrid de novo whole genome sequencing and digital DNA-DNA hybridization, isolate WUR7 was identified as a novel species from the Gram-negative genus Lacinutrix. Its genome was mined for the presence of biosynthetic gene clusters with limited results. However, extensive investigation of its metabolism uncovered an unusual tryptophan decarboxylase with high sequence homology and conserved structure of the active site as compared to ZP_02040762, a highly specific tryptophan decarboxylase from Ruminococcus gnavus. Therefore, WUR7's metabolism was directed toward indole-based alkaloid biosynthesis by feeding it with L-tryptophan. As expected, its metabolome profile changed dramatically, by triggering the extracellular accumulation of a massive array of metabolites unexpressed in the absence of tryptophan. Untargeted LC-MS/MS coupled with molecular networking, followed along with chemoinformatic dereplication, allowed for the annotation of 10 indole alkaloids, belonging to β-carboline, bisindole, and monoindole classes, alongside several unknown alkaloids. These findings guided us to the isolation of a new natural bisindole alkaloid 8,9-dihydrocoscinamide B (1), as the first alkaloid from the genus Lacinutrix, whose structure was elucidated on the basis of extensive 1D and 2D NMR and HR-ESIMS experiments. This comprehensive strategy allowed us to unlock the previously unexploited metabolome of L. shetlandiensis sp. nov. WUR7.

Keywords: Lacinutrix; OMICs; OSMAC; alkaloids; deep sea.