Marine actinomycetes belonging to the genus Salinispora have proven to be a rich source of novel secondary metabolites including one compound (salinosporamide A) that is currently in clinical trials for the treatment of cancer. Despite extensive fermentation studies of S. tropica and S. arenicola, recent genome sequencing has revealed an abundance of novel biosynthetic gene clusters in both taxa whose products have yet to be discovered. This new information provides clear evidence that even these well-studied environmental bacteria continue to represent an important resource for natural product discovery. We have amassed a large collection of several thousand Salinispora isolates from numerous worldwide collection sites that produce distinct suites of secondary metabolites indicating that the overall breadth of biosynthetic diversity within the genus is far greater than previously recognized. We are now presented with a unique opportunity to combine the powerful techniques of genome sequence analysis, along with the ability to genetically manipulate Salinispora in the laboratory, to integrate bacterial genetics into the natural product drug discovery process. We therefore propose a comprehensive and multi-disciplinary program in which innovative genome mining techniques will be employed to effectively enhance the discovery of natural products from this new group of marine bacteria. To accomplish the broad goals outlined in this application, the Moore and Jensen laboratories have established a long-term collaboration that seamlessly integrates the complementary expertise of both research programs. We propose two major aims. First, we will isolate, characterize, and test for biological activity new natural products from S. tropica strain CNB-440 and S. arenicola CNS-205 discovered through bioinformatics-based, genome mining techniques. From our comprehensive genome sequencing and annotation of both strains, we have identified five orphan gene sets to explore that have a high probability to yield novel metabolites with promising biological properties and novel enzymatic mechanisms in natural product biosynthesis. Second, we will sequence and annotate draft genomes of four new Salinispora strains, including two phylotypes of the new species S. pacifica and two geographically and metabolically distinct S. arenicola strains, and mine them for the production of novel secondary metabolites.

Public Health Relevance

Natural microbial products occupy a central role in medicine by providing the majority of the antibiotics and anticancer agents employed in the clinic as well as important biomedical research tools used to discover and probe cellular processes. As the discovery rate of new chemical entities from bacteria diminishes over time, innovative methods are urgently needed to provide new molecular scaffolds from which drug leads can be developed. By combining a new marine bacterial resource that has a proven track record in providing clinically relevant drug candidates together with a comprehensive natural product discovery approach that employs innovative analyses of microbial genome sequences and state of the art genetic manipulation, we aim to unlock the biosynthetic potential of a select group of bacteria and provide new compounds for biological testing. These molecules have the potential to be developed into new anticancer agents or antibiotics, or provide the structural motifs from which such drugs can be developed. Public health may directly benefit from these discoveries or, in the long term, from advances in the efficiency of the natural product discovery process that will be gained from this research.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
Project #
Application #
Study Section
Synthetic and Biological Chemistry B Study Section (SBCB)
Program Officer
Jones, Warren
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
University of California San Diego
Schools of Earth Sciences/Natur
La Jolla
United States
Zip Code
Zhang, Jia Jia; Moore, Bradley S; Tang, Xiaoyu (2018) Engineering Salinispora tropica for heterologous expression of natural product biosynthetic gene clusters. Appl Microbiol Biotechnol 102:8437-8446
Reynolds, Kirk A; Luhavaya, Hanna; Li, Jie et al. (2018) Isolation and structure elucidation of lipopeptide antibiotic taromycin B from the activated taromycin biosynthetic gene cluster. J Antibiot (Tokyo) 71:333-338
Schlawis, Christian; Kern, Simone; Kudo, Yuta et al. (2018) Structural Elucidation of Trace Components Combining GC/MS, GC/IR, DFT-Calculation and Synthesis-Salinilactones, Unprecedented Bicyclic Lactones from Salinispora Bacteria. Angew Chem Int Ed Engl 57:14921-14925
Bruns, Hilke; Crüsemann, Max; Letzel, Anne-Catrin et al. (2018) Function-related replacement of bacterial siderophore pathways. ISME J 12:320-329
Gallagher, Kelley A; Wanger, Greg; Henderson, Jane et al. (2017) Ecological implications of hypoxia-triggered shifts in secondary metabolism. Environ Microbiol 19:2182-2191
Machado, Henrique; Tuttle, Robert N; Jensen, Paul R (2017) Omics-based natural product discovery and the lexicon of genome mining. Curr Opin Microbiol 39:136-142
Crüsemann, Max; O'Neill, Ellis C; Larson, Charles B et al. (2017) Prioritizing Natural Product Diversity in a Collection of 146 Bacterial Strains Based on Growth and Extraction Protocols. J Nat Prod 80:588-597
Zhang, Jia Jia; Tang, Xiaoyu; Zhang, Michelle et al. (2017) Broad-Host-Range Expression Reveals Native and Host Regulatory Elements That Influence Heterologous Antibiotic Production in Gram-Negative Bacteria. MBio 8:
Letzel, Anne-Catrin; Li, Jing; Amos, Gregory C A et al. (2017) Genomic insights into specialized metabolism in the marine actinomycete Salinispora. Environ Microbiol 19:3660-3673
Millán-Aguiñaga, Natalie; Chavarria, Krystle L; Ugalde, Juan A et al. (2017) Phylogenomic Insight into Salinispora (Bacteria, Actinobacteria) Species Designations. Sci Rep 7:3564

Showing the most recent 10 out of 59 publications