Imaging mass spectrometry in microbiology

Watrous, Jeramie D.; Dorrestein, Pieter C.

doi:10.1038/nrmicro2634

Cited by 295 publications

(302 citation statements)

References 86 publications

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“…Although individual steps of the present procedure have been used previously in natural product research (15,19,47,(50)(51)(52), the combination of methods has not been reported and should be applicable to many further organisms. The 13 C-NMR-based technique and other recent methods such as imaging MS (53) can detect low concentration signatures of nosperin and facilitate investigation of its role in symbiosis. These approaches could also identify molecular variants: e.g., recently studied specimens of P. membranacea that appear negative for only one or two of the three primer sets used for nsp screening may present variants of nosperin.…”

Section: Discussionmentioning

confidence: 99%

Metagenomic natural product discovery in lichen provides evidence for a family of biosynthetic pathways in diverse symbioses

Kampa

Gagunashvili

Gulder

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

125

127

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Bacteria are a major source of natural products that provide rich opportunities for both chemical and biological investigation. Although the vast majority of known bacterial metabolites derive from free-living organisms, increasing evidence supports the widespread existence of chemically prolific bacteria living in symbioses. A strategy based on bioinformatic prediction, symbiont cultivation, isotopic enrichment, and advanced analytics was used to characterize a unique polyketide, nosperin, from a lichen-associated Nostoc sp. cyanobacterium. The biosynthetic gene cluster and the structure of nosperin, determined from 30 μg of compound, are related to those of the pederin group previously known only from nonphotosynthetic bacteria associated with beetles and marine sponges. The presence of this natural product family in such highly dissimilar associations suggests that some bacterial metabolites may be specific to symbioses with eukaryotes and encourages exploration of other symbioses for drug discovery and better understanding of ecological interactions mediated by complex bacterial metabolites.biosynthesis | Peltigera membranacea | trans-acyltransferase polyketide synthase | 13 C nuclear magnetic resonance

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Section: Discussionmentioning

confidence: 99%

Metagenomic natural product discovery in lichen provides evidence for a family of biosynthetic pathways in diverse symbioses

Kampa

Gagunashvili

Gulder

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

125

127

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“…Mg1 (S. Mg1), in a competitive interaction with B. subtilis. To follow the fates of surfactin and other natural products in competition with S. Mg1, a MALDI-TOF-based imaging mass spectrometry (IMS) approach was used (31,38,39). IMS provided a method to track in situ the secretion and modification of surfactin during interspecies interactions.…”

mentioning

confidence: 99%

Enzymatic resistance to the lipopeptide surfactin as identified through imaging mass spectrometry of bacterial competition

Hoefler

Gorzelnik

Yang

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

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Many species of bacteria secrete natural products that inhibit the growth or development of competing species. In turn, competitors may develop or acquire resistance to antagonistic molecules. Few studies have investigated the interplay of these countervailing forces in direct competition between two species. We have used an imaging mass spectrometry (IMS) approach to track metabolites exchanged between Bacillus subtilis and Streptomyces sp. Mg1 cultured together. Surfactin is a cyclic lipopeptide produced by B. subtilis that inhibits the formation of aerial hyphae by streptomycetes. IMS analysis exposed an addition of 18 mass units to surfactin in the agar proximal to Streptomyces sp. Mg1 but not other streptomycetes tested. The spatially resolved change in the mass of surfactin indicated hydrolysis of the molecule. We observed that the aerial growth of Streptomyces sp. Mg1 was resistant to inhibition by surfactin, which suggests that hydrolysis was a mechanism of resistance. To identify possible enzymes from Streptomyces sp. Mg1 with surfactin hydrolase activity, we isolated secreted proteins and identified candidates by mass spectrometry. We purified one candidate enzyme that hydrolyzed surfactin in vitro. We tested the role of this enzyme in surfactin resistance by deleting the corresponding gene from the S . Mg1 genome. We observed that aerial growth by the Δ sfhA mutant strain was now sensitive to surfactin. Our results identify an enzyme that hydrolyzes surfactin and confers resistance to aerial growth inhibition, which demonstrates the effective use of an IMS approach to track natural product modifications during interspecies competition.

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“…Future studies may incorporate also micro scale observations , which have become possible through a variety of novel analytical techniques (e.g. BrehmStecher and Johnson, 2004;Müller and Nebe-von-Caron, 2010;Watrous and Dorrestein, 2011). Such observational data can be beneficial as direct input (providing parameter values or initial conditions), but also for inverse modeling (being compared to emergent model output to derive parameter values or process definitions).…”

Section: Applications and Perspectivesmentioning

confidence: 99%

Individual-based modeling of soil organic matter in NetLogo: Transparent, user-friendly, and open

Banitz

Gras

Gisbert

2015

Environmental Modelling & Software

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Soil organic matter dynamics are essential for terrestrial ecosystem functions as they affect biogeochemical cycles and, thus, the provision of plant nutrients or the release of greenhouse gases to the atmosphere. Most of the involved processes are driven by microorganisms. To investigate and understand these processes, individual-based models allow analyzing complex microbial systems' behavior based on rules and conditions for individual entities within these systems, taking into account local interactions and individual variations. Here, we present a 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 3 HighlightsWe present a NetLogo version of an established IBM of SOM dynamics driven by microbes.The model was made simpler and less specific to increase its application potential.Users may easily access, explore and also modify the computational model.We provide the first complete standardized model description of INDISIM-SOM.The overall aim is an improved understanding of carbon and nitrogen dynamics in soils.

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Imaging mass spectrometry in microbiology

Cited by 295 publications

References 86 publications

Metagenomic natural product discovery in lichen provides evidence for a family of biosynthetic pathways in diverse symbioses

Metagenomic natural product discovery in lichen provides evidence for a family of biosynthetic pathways in diverse symbioses

Enzymatic resistance to the lipopeptide surfactin as identified through imaging mass spectrometry of bacterial competition

Individual-based modeling of soil organic matter in NetLogo: Transparent, user-friendly, and open

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