This renewal application builds upon a productive collaboration between the Moore (biosynthesis/natural products chemistry) and Jensen (bioinformatics/microbiology) labs. It seeks to capitalize on the biosynthetic potential maintained in bacterial genomes by developing three specific areas of research: 1) Transcriptome guided natural product discovery, 2) Heterologous expression, production, and characterization of Salinispora secondary metabolites, and 3) Characterization and exploitation of secondary metabolite regulation. The research will be implemented using the model marine actinomycete genus Salinispora, for which a unique culture collection and a large number of genome sequences are available. Comparative transcriptomics will be used to distinguish between silentandexpressedgeneclusters,identifykeyregulatoryelementsassociatedwiththeirsilencing,and prioritize clusters for heterologous expression and product characterization. The resulting compounds will be isolated, characterized, and subjected to biological testing. A workflow has been developed to target gene clusters that possess the highest probability to yield structurally unique and biologically active compounds. The mechanistic enzymology associated with unique structural features will be interrogated and used to inform future structure predictions. This project will specifically address the regulation of secondary metabolism by testing the effects of salinipostin as an A-factor-like regulator, identifying the genetic basis for a spontaneous, pigment-less mutant that is reduced in secondary metabolite production, and introducing regulatory elements whose disruption has been linked to gene clustersilencinginspecificstrains.Thefundamentalgoalsaretodevelopnewtoolsandapproachesto identify the natural products encoded in bacterial genomes, obtain new information about the mechanistic biochemistry responsible for their assembly, and to develop more efficient approaches to minebacterialgenomesforthestructurallyuniqueandbiologicallyactivecompoundstheyencode.The research effectively combines the complimentary expertise of two research groups in the areas of marinemicrobiology,biosynthesis,andnaturalproductdiscovery.

Public Health Relevance

Thisresearchdevelopsandappliesadvancedapproachestocapitalizeonthewealthof biosynthetic potential maintained in bacterial genomes. New tools in synthetic biology will be employed and the mechanisms that regulate natural product biosynthesis investigatedinanefforttodiscovernewnaturalproductsandcharacterizetheenzymes responsible for their biosynthesis. Isolated compounds will be tested for medicinally relevant biological activities and the knowledge gained used to advance our basic understandingofthemechanismsofnaturalproductbiosynthesis.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
2R01GM085770-09
Application #
9389659
Study Section
Synthetic and Biological Chemistry B Study Section (SBCB)
Program Officer
Fabian, Miles
Project Start
2009-08-01
Project End
2021-07-31
Budget Start
2017-08-01
Budget End
2018-07-31
Support Year
9
Fiscal Year
2017
Total Cost
Indirect Cost
Name
University of California, San Diego
Department
Zoology
Type
Earth Sciences/Resources
DUNS #
804355790
City
La Jolla
State
CA
Country
United States
Zip Code
92093
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

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