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Pathirana, C, Dwight R, Jensen PR, Fenical W, Delgado A, Brinen LS, Clardy J.  1991.  Structure and Synthesis of a New Butanolide from a Marine Actinomycete. Tetrahedron Letters. 32:7001-7004.   10.1016/0040-4039(91)85024-y   AbstractWebsite

The novel butanolide 2, (1'R, 2S, 4S)-2-(1-hydroxy-6-methylheptyl)-4-hydroxymethyl-butanolide, was isolated from the culture broth of a marine actinomycete. The structure of 2 was assigned by analysis of spectral data and the absolute configuration was determined by synthesis.

Pathirana, C, Jensen PR, Fenical W.  1992.  Marinone and Debromomarinone - Antibiotic Sesquiterpenoid Naphthoquinones of a New Structure Class from a Marine Bacterium. Tetrahedron Letters. 33:7663-7666.   10.1016/0040-4039(93)88010-g   AbstractWebsite

Marinone (1) and its debromo analog debromomarinone (2), antibiotic sesquiterpenoid naphthoquinones of a new structure class, have been isolated from the organic extract of the liquid culture of a marine actinomycete, isolate CNB-632. The structures of the new compounds were assigned on the basis of comprehensive spectroscopic analyses.

Pathirana, C, Tapiolas D, Jensen PR, Dwight R, Fenical W.  1991.  Structure Determination of Maduralide - a New 24-Membered Ring Macrolide Glycoside Produced by a Marine Bacterium (Actinomycetales). Tetrahedron Letters. 32:2323-2326.   10.1016/s0040-4039(00)79914-x   AbstractWebsite

Maduralide (1), a novel macrolide possessing a 24-membered ring, was isolated from a marine bacterium grown in liquid culture. The structure of this new metabolite was determined by spectroscopic methods.

Pathirana, C, Jensen PR, Dwight R, Fenical W.  1992.  Rare Phenazine L-Quinovose Esters from a Marine Actinomycete. Journal of Organic Chemistry. 57:740-742.   10.1021/jo00028a060   Website
Patin, NV, Schorn M, Aguinaldo K, Lincecum T, Moore BS, Jensen PR.  2017.  Effects of actinomycete secondary metabolites on sediment microbial communities. Applied and Environmental Microbiology. 83   10.1128/aem.02676-16   Abstract

Marine sediments harbor complex microbial communities that remain poorly studied relative to other biomes such as seawater. Moreover, bacteria in these communities produce antibiotics and other bioactive secondary metabolites, yet little is known about how these compounds affect microbial community structure. In this study, we used next-generation amplicon sequencing to assess native microbial community composition in shallow tropical marine sediments. The results revealed complex communities comprised of largely uncultured taxa, with considerable spatial heterogeneity and known antibiotic producers comprising only a small fraction of the total diversity. Organic extracts from cultured strains of the sedimentdwelling actinomycete genus Salinispora were then used in mesocosm studies to address how secondary metabolites shape sediment community composition. We identified predatory bacteria and other taxa that were consistently reduced in the extract-treated mesocosms, suggesting that they may be the targets of allelopathic interactions. We tested related taxa for extract sensitivity and found general agreement with the culture-independent results. Conversely, several taxa were enriched in the extract-treated mesocosms, suggesting that some bacteria benefited from the interactions. The results provide evidence that bacterial secondary metabolites can have complex and significant effects on sediment microbial communities. IMPORTANCE Ocean sediments represent one of Earth's largest and most poorly studied biomes. These habitats are characterized by complex microbial communities where competition for space and nutrients can be intense. This study addressed the hypothesis that secondary metabolites produced by the sediment-inhabiting actinomycete Salinispora arenicola affect community composition and thus mediate interactions among competing microbes. Next-generation amplicon sequencing of mesocosm experiments revealed complex communities that shifted following exposure to S. arenicola extracts. The results reveal that certain predatory bacteria were consistently less abundant following exposure to extracts, suggesting that microbial metabolites mediate competitive interactions. Other taxa increased in relative abundance, suggesting a benefit from the extracts themselves or the resulting changes in the community. This study takes a first step toward assessing the impacts of bacterial metabolites on sediment microbial communities. The results provide insight into how low-abundance organisms may help structure microbial communities in ocean sediments.

Patin, NV, Floros DJ, Hughes CC, Dorrestein PC, Jensen PR.  2018.  The role of inter-species interactions in Salinispora specialized metabolism. Microbiology-Sgm. 164:946-955.   10.1099/mic.0.000679   AbstractWebsite

Bacterial genome sequences consistently contain many more biosynthetic gene clusters encoding specialized metabolites than predicted by the compounds discovered from the respective strains. One hypothesis invoked to explain the cryptic nature of these gene clusters is that standard laboratory conditions do not provide the environmental cues needed to trigger gene expression. A potential source of such cues is other members of the bacterial community, which are logical targets for competitive interactions. In this study, we examined the effects of such interactions on specialized metabolism in the marine actinomycete Salinispora tropica. The results show that antibiotic activities and the concentration of some small molecules increase in the presence of co-occurring bacterial strains relative to monocultures. Some increases in antibiotic activity could be linked to nutrient depletion by the competitor as opposed to the production of a chemical cue. Other increases were correlated with the production of specific compounds by S. tropica. In particular, one interaction with a Vibrio sp. consistently induced antibiotic activity and was associated with parent ions that were unique to this interaction, although the associated compound could not be identified. This study provides insight into the metabolomic complexities of bacterial interactions and baseline information for future genome mining efforts.

Patin, NV, Duncan KR, Dorrestein PC, Jensen PR.  2016.  Competitive strategies differentiate closely related species of marine actinobacteria. Isme Journal. 10:478-490.   10.1038/ismej.2015.128   AbstractWebsite

Although competition, niche partitioning, and spatial isolation have been used to describe the ecology and evolution of macro-organisms, it is less clear to what extent these principles account for the extraordinary levels of bacterial diversity observed in nature. Ecological interactions among bacteria are particularly challenging to address due to methodological limitations and uncertainties over how to recognize fundamental units of diversity and link them to the functional traits and evolutionary processes that led to their divergence. Here we show that two closely related marine actinomycete species can be differentiated based on competitive strategies. Using a direct challenge assay to investigate inhibitory interactions with members of the bacterial community, we observed a temporal difference in the onset of inhibition. The majority of inhibitory activity exhibited by Salinispora arenicola occurred early in its growth cycle and was linked to antibiotic production. In contrast, most inhibition by Salinispora tropica occurred later in the growth cycle and was more commonly linked to nutrient depletion or other sources. Comparative genomics support these differences, with S. arenicola containing nearly twice the number of secondary metabolite biosynthetic gene clusters as S. tropica, indicating a greater potential for secondary metabolite production. In contrast, S. tropica is enriched in gene clusters associated with the acquisition of growth-limiting nutrients such as iron. Coupled with differences in growth rates, the results reveal that S. arenicola uses interference competition at the expense of growth, whereas S. tropica preferentially employs a strategy of exploitation competition. The results support the ecological divergence of two co-occurring and closely related species of marine bacteria by providing evidence they have evolved fundamentally different strategies to compete in marine sediments.

Penn, K, Jenkins C, Nett M, Udwary DW, Gontang EA, McGlinchey RP, Foster B, Lapidus A, Podell S, Allen EE, Moore BS, Jensen PR.  2009.  Genomic islands link secondary metabolism to functional adaptation in marine Actinobacteria. Isme Journal. 3:1193-1203.   10.1038/ismej.2009.58   AbstractWebsite

Genomic islands have been shown to harbor functional traits that differentiate ecologically distinct populations of environmental bacteria. A comparative analysis of the complete genome sequences of the marine Actinobacteria Salinispora tropica and Salinispora arenicola reveals that 75% of the species-specific genes are located in 21 genomic islands. These islands are enriched in genes associated with secondary metabolite biosynthesis providing evidence that secondary metabolism is linked to functional adaptation. Secondary metabolism accounts for 8.8% and 10.9% of the genes in the S. tropica and S. arenicola genomes, respectively, and represents the major functional category of annotated genes that differentiates the two species. Genomic islands harbor all 25 of the species-specific biosynthetic pathways, the majority of which occur in S. arenicola and may contribute to the cosmopolitan distribution of this species. Genome evolution is dominated by gene duplication and acquisition, which in the case of secondary metabolism provide immediate opportunities for the production of new bioactive products. Evidence that secondary metabolic pathways are exchanged horizontally, coupled with earlier evidence for fixation among globally distributed populations, supports a functional role and suggests that the acquisition of natural product biosynthetic gene clusters represents a previously unrecognized force driving bacterial diversification. Species-specific differences observed in clustered regularly interspaced short palindromic repeat sequences suggest that S. arenicola may possess a higher level of phage immunity, whereas a highly duplicated family of polymorphic membrane proteins provides evidence for a new mechanism of marine adaptation in Gram-positive bacteria. The ISME Journal (2009) 3, 1193-1203; doi:10.1038/ismej.2009.58; published online 28 May 2009

Penn, K, Jensen PR.  2012.  Comparative genomics reveals evidence of marine adaptation in Salinispora species. BMC Genomics. 13   10.1186/1471-2164-13-86   AbstractWebsite

Background: Actinobacteria represent a consistent component of most marine bacterial communities yet little is known about the mechanisms by which these Gram-positive bacteria adapt to life in the marine environment. Here we employed a phylogenomic approach to identify marine adaptation genes in marine Actinobacteria. The focus was on the obligate marine actinomycete genus Salinispora and the identification of marine adaptation genes that have been acquired from other marine bacteria. Results: Functional annotation, comparative genomics, and evidence of a shared evolutionary history with bacteria from hyperosmotic environments were used to identify a pool of more than 50 marine adaptation genes. An Actinobacterial species tree was used to infer the likelihood of gene gain or loss in accounting for the distribution of each gene. Acquired marine adaptation genes were associated with electron transport, sodium and ABC transporters, and channels and pores. In addition, the loss of a mechanosensitive channel gene appears to have played a major role in the inability of Salinispora strains to grow following transfer to low osmotic strength media. Conclusions: The marine Actinobacteria for which genome sequences are available are broadly distributed throughout the Actinobacterial phylogenetic tree and closely related to non-marine forms suggesting they have been independently introduced relatively recently into the marine environment. It appears that the acquisition of transporters in Salinispora spp. represents a major marine adaptation while gene loss is proposed to play a role in the inability of this genus to survive outside of the marine environment. This study reveals fundamental differences between marine adaptations in Gram-positive and Gram-negative bacteria and no common genetic basis for marine adaptation among the Actinobacteria analyzed.

Pimentel-Elardo, S, Wehrl M, Friedrich AB, Jensen PR, Hentschel U.  2003.  Isolation of planctomycetes from Aplysina sponges. Aquatic Microbial Ecology. 33:239-245.   10.3354/ame033239   AbstractWebsite

There is mounting molecular evidence that bacteria belonging to the phylum Planctomycetes are abundant in marine sponges including members of the genus Aplysina. In an attempt to culture planctomycete bacteria from Aplysina sponges, 116 bacterial strains were isolated on selective oligotrophic media. Screening of the strain collection by fluorescence in situ hybridization with the planctomycete-specific probe Pla46 yielded 3 positive candidates. Nearly complete sequencing of the respective 16S rRNA genes revealed that the isolates were affiliated with 2 distinct clusters of the genus Pirellula: 1 isolate was obtained from a Mediterranean sponge, 1 from a Caribbean sponge and a third from Caribbean seawater. To our knowledge this is the first report of cultured Planctomycetes from marine sponges. The isolates grew slowly on oligotrophic media and failed to grow on nutrient-rich media. Pirellula sp. Strain 797 was pink-pigmented while the other 2 isolates, 16 and 81, were non-pigmented. Transmission electron microscopy revealed a pear- or droplet-shaped cell morphology that is characteristic of the genus Pirellula. The application of strain-specific oligonucleotide probes to sponge tissue cryosections showed that the isolates contribute only a minor fraction to the total microbial community that is associated with Aplysina spp. sponges.

Potts, BC, Albitar MX, Anderson KC, Baritaki S, Berkers C, Bonavida B, Chandra J, Chauhan D, Cusack JC, Fenical W, Ghobrial IM, Groll M, Jensen PR, Lam KS, Lloyd GK, McBride W, McConkey DJ, Miller CP, Neuteboom STC, Oki Y, Ovaa H, Pajonk F, Richardson PG, Roccaro AM, Sloss CM, Spear MA, Valashi E, Younes A, Palladino MA.  2011.  Marizomib, a Proteasome Inhibitor for All Seasons: Preclinical Profile and a Framework for Clinical Trials. Current Cancer Drug Targets. 11:254-284. AbstractWebsite

The proteasome has emerged as an important clinically relevant target for the treatment of hematologic malignancies. Since the Food and Drug Administration approved the first-in-class proteasome inhibitor bortezomib (Velcade (R)) for the treatment of relapsed/refractory multiple myeloma (MM) and mantle cell lymphoma, it has become clear that new inhibitors are needed that have a better therapeutic ratio, can overcome inherent and acquired bortezomib resistance and exhibit broader anti-cancer activities. Marizomib (NPI-0052; salinosporamide A) is a structurally and pharmacologically unique beta-lactone-gamma-lactam proteasome inhibitor that may fulfill these unmet needs. The potent and sustained inhibition of all three proteolytic activities of the proteasome by marizomib has inspired extensive preclinical evaluation in a variety of hematologic and solid tumor models, where it is efficacious as a single agent and in combination with biologics, chemotherapeutics and targeted therapeutic agents. Specifically, marizomib has been evaluated in models for multiple myeloma, mantle cell lymphoma, Waldenstrom's macroglobulinemia, chronic and acute lymphocytic leukemia, as well as glioma, colorectal and pancreatic cancer models, and has exhibited synergistic activities in tumor models in combination with bortezomib, the immunomodulatory agent lenalidomide (Revlimid (R)), and various histone deacetylase inhibitors. These and other studies provided the framework for ongoing clinical trials in patients with MM, lymphomas, leukemias and solid tumors, including those who have failed bortezomib treatment, as well as in patients with diagnoses where other proteasome inhibitors have not demonstrated significant efficacy. This review captures the remarkable translational studies and contributions from many collaborators that have advanced marizomib from seabed to bench to bedside.

Prieto-Davo, A, Villarreal-Gomez LJ, Forschner-Dancause S, Bull AT, Stach JEM, Smith DC, Rowley DC, Jensen PR.  2013.  Targeted search for actinomycetes from nearshore and deep-sea marine sediments. Fems Microbiology Ecology. 84:510-518.   10.1111/1574-6941.12082   AbstractWebsite

Sediment samples collected off the coast of San Diego were analyzed for actinomycete diversity using culture-independent techniques. Eight new operational taxonomic units (OTUs) in the Streptomycetaceae were identified as well as new diversity within previously cultured marine OTUs. Sequences belonging to the marine actinomycete genus Salinispora were also detected, despite the fact that this genus has only been reported from more tropical environments. Independent analyses of marine sediments from the Canary Basin (3814m) and the South Pacific Gyre (5126 and 5699m) also revealed Salinispora sequences providing further support for the occurrence of this genus in deep-sea sediments. Efforts to culture Salinispora spp. from these samples have yet to be successful. This is the first report of Salinispora spp. from marine sediments >1100m and suggests that the distribution of this genus is broader than previously believed.

Prieto-Davo, A, Fenical W, Jensen PR.  2008.  Comparative actinomycete diversity in marine sediments. Aquatic Microbial Ecology. 52:1-11.   10.3354/ame01211   AbstractWebsite

The diversity of cultured actinomycete bacteria was compared between near- and offshore marine sediments. Strains were tested for the effects of seawater on growth and analyzed for 16S rRNA gene sequence diversity. In total, 623 strains representing 6 families in the order Actinomycetales were cultured. These strains were binned into 16 to 63 operational taxonomic units (OTUs) over a range of 97 to 100 % sequence identity. The majority of the OTUs were closely related (> 98 % sequence identity) to strains previously reported from non-marine sources; indicating that most are not restricted to the sea. However, new OTUs averaged 96.6 % sequence identity with previously cultured strains and ca. one-third of the OTUs were marine-specific, suggesting that sediment communities include considerable actinomycete diversity that does not occur on land. Marine specificity did not increase at the off-shore sites, indicating high levels of terrestrial influence out to 125 km from shore. The requirement of seawater for growth was observed among < 6%. of the strains, while all members of 9 OTUs possessed this trait, revealing a high degree of marine adaptation among some lineages. Statistical analyses predicted greater OTU diversity at the off-shore sites and provided a rationale for expanded exploration of deep-sea samples. A change in community composition was observed, with the number of Micromonospora OTUs increasing in the off-shore samples. UniFrac (see http://bmf2.colorado.edu/unifrac) statistics support a difference in community composition between near- and off-shore locations. Overall, 123 of 176 strains had distinct 16S rRNA gene sequences, indicating a high level of actinomycete diversity in marine sediments.

Prudhomme, J, McDaniel E, Ponts N, Bertani S, Fenical W, Jensen P, Le Roch K.  2008.  Marine Actinomycetes: A New Source of Compounds against the Human Malaria Parasite. Plos One. 3   10.1371/journal.pone.0002335   AbstractWebsite

Background: Malaria continues to be a devastating parasitic disease that causes the death of 2 million individuals annually. The increase in multi-drug resistance together with the absence of an efficient vaccine hastens the need for speedy and comprehensive antimalarial drug discovery and development. Throughout history, traditional herbal remedies or natural products have been a reliable source of antimalarial agents, e. g. quinine and artemisinin. Today, one emerging source of small molecule drug leads is the world's oceans. Included among the source of marine natural products are marine microorganisms such as the recently described actinomycete. Members of the genus Salinispora have yielded a wealth of new secondary metabolites including salinosporamide A, a molecule currently advancing through clinical trials as an anticancer agent. Because of the biological activity of metabolites being isolated from marine microorganisms, our group became interested in exploring the potential efficacy of these compounds against the malaria parasite. Methods: We screened 80 bacterial crude extracts for their activity against malaria growth. We established that the pure compound, salinosporamide A, produced by the marine actinomycete, Salinispora tropica, shows strong inhibitory activity against the erythrocytic stages of the parasite cycle. Biochemical experiments support the likely inhibition of the parasite 20S proteasome. Crystal structure modeling of salinosporamide A and the parasite catalytic 20S subunit further confirm this hypothesis. Ultimately we showed that salinosporamide A protected mice against deadly malaria infection when administered at an extremely low dosage. Conclusion: These findings underline the potential of secondary metabolites, derived from marine microorganisms, to inhibit Plasmodium growth. More specifically, we highlight the effect of proteasome inhibitors such as salinosporamide A on in vitro and in vivo parasite development. Salinosporamide A (NPI-0052) now being advanced to phase I trials for the treatment of refractory multiple myeloma will need to be further explored to evaluate the safety profile for its use against malaria.

Puglisi, MP, Engel S, Jensen PR, Fenical W.  2007.  Antimicrobial activities of extracts from Indo-Pacific marine plants against marine pathogens and saprophytes. Marine Biology. 150:531-540.   10.1007/s00227-006-0376-3   AbstractWebsite

This study is the second of two surveys designed to systematically screen extracts from marine plants for antimicrobial effects against ecologically relevant marine microorganisms, and to compare results on a geographical basis. In the preceding survey, extracts from tropical Atlantic marine algae and seagrasses were screened in growth inhibition assays against the pathogenic fungus Lindra thalassiae, the saprophytic fungus Dendryphiella salina, the saprophytic stramenopiles, Halophytophthora spinosa and Schizochytrium aggregatum, and the pathogenic bacterium Pseudoaltermonas bacteriolytica. In this study, the same assay microorganisms were used to examine the antimicrobial effects of lipophilic and hydrophilic extracts from 54 species of marine algae and two species of seagrasses collected from Indo-Pacific reef habitats. Overall, 95% of all species surveyed in this study yielded extracts that were active against one or more, and 77% yielded extracts that were active against two or more assay microorganisms. Broad-spectrum activity against three or four assay microbes was observed in the extracts from 50 to 21% of all species, respectively. Extracts from the green alga Bryopsis pennata and the red alga Portieria hornemannii inhibited the growth of all assay microorganisms. Given that antimicrobial activity was prevalent among extracts of Indo-Pacific marine plants, it is interesting to note that the inhibitory effects of each extract varied considerably between the assay microorganisms. Overall, H. spinosa and D. salina were the most susceptible while L. thalassiae, S. aggregatum, and P. bacteriolytica were the most resistant to the extracts tested. These results provide good evidence that antimicrobial chemical defenses are widespread among Indo-Pacific marine plants. Further, the activity profiles of plant extracts suggest that antimicrobial secondary metabolites can have pathogen-selective or broad-spectrum effects. To confirm these results, chemical studies will be needed to isolate and characterize the compounds responsible for the observed antimicrobial activities.

Puglisi, MP, Tan LT, Jensen PR, Fenical W.  2004.  Capisterones A and B from the tropical green alga Penicillus capitatus: unexpected anti-fungal defenses targeting the marine pathogen Lindra thallasiae. Tetrahedron. 60:7035-7039.   10.1016/j.tet.2003.10.131   AbstractWebsite

The mechanism by which marine algae show resistance to pathogenic microorganisms remains poorly understood. To examine the possible role that algal secondary metabolites play in the prevention of infection, we examined the abundant green alga Penicillus capitatus, one of the major shallow water algae found in the Tropical Atlantic Ocean. Both aqueous and EtOAc extracts of this alga were found to be potent inhibitors of the well-known marine algal pathogen Lindra thallasiae. Using L. thallasiae in bioassay-guided fractionation, we isolated two new triterpene sulfate esters, capisterones A (1) and B (2). The capisterones are potent inhibitors of L. thallasiae at natural and below natural concentrations. The structures of the capisterones, with relative stereochemistry only, were assigned by comprehensive spectral analyses that relied heavily on 2D NMR methods. (C) 2004 Elsevier Ltd. All rights reserved.