Primer on Agar-Based Microbial Imaging Mass Spectrometry

Journal of Bacteriology - Tập 194 Số 22 - Trang 6023-6028 - 2012
Jane Y. Yang1, Vanessa V. Phelan2, Ryan Simkovsky3, Jeramie D. Watrous1, Rachelle M. Trial4, Tinya C. Fleming4, Roland Wenter5, Bradley S. Moore5,2, Susan S. Golden3, Kit Pogliano4, Pieter C. Dorrestein1,6,2
1Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California, USA
2Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, California, USA
3Center for Chronobiology, Division of Biological Sciences, University of California at San Diego, La Jolla, California, USA
4Division of Biological Sciences, University of California at San Diego, La Jolla, California, USA
5Scripps Institution of Oceanography, University of California at San Diego, La Jolla, California, USA
6Department of Pharmacology, University of California at San Diego, La Jolla, California, USA

Tóm tắt

ABSTRACT Matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) imaging mass spectrometry (IMS) applied directly to microbes on agar-based medium captures global information about microbial molecules, allowing for direct correlation of chemotypes to phenotypes. This tool was developed to investigate metabolic exchange factors of intraspecies, interspecies, and polymicrobial interactions. Based on our experience of the thousands of images we have generated in the laboratory, we present five steps of microbial IMS: culturing, matrix application, dehydration of the sample, data acquisition, and data analysis/interpretation. We also address the common challenges encountered during sample preparation, matrix selection and application, and sample adherence to the MALDI target plate. With the practical guidelines described herein, microbial IMS use can be extended to bio-based agricultural, biofuel, diagnostic, and therapeutic discovery applications.

Từ khóa


Tài liệu tham khảo

AlaupovicP OlsonAC TsangJ. 1966. Studies on the characterization of lipopolysaccharides from two strains of Serratia marcescens. Ann. N. Y. Acad. Sci. 133:546–565.

AnandS. 2010. SBSPKS: structure based sequence analysis of polyketide synthases. Nucleic Acids Res. 38:W487–W496.

AnsariMZ YadavG GokhaleRS MohantyD. 2004. NRPS-PKS: a knowledge-based resource for analysis of NRPS/PKS megasythases. Nucleic Acids Res. 32:W405–W413.

10.1099/mic.0.038794-0

ArimaK KakinumaA TamuraG. 1968. Surfactin, a crystalline peptidelipid surfactant produced by Bacillus subtilis: isolation, characterization and its inhibition of fibrin clot formation. Biochem. Biophys. Res. Commun. 31:488–494.

10.1016/j.cell.2006.04.001

10.1128/AEM.00730-09

BowenBP NorthenT. 2010. Dealing with the unknown: metabolomics and metabolite atlases. J. Am. Soc. Mass Spectrom. 21:1471–1476.

10.1073/pnas.191384198

10.1128/jb.173.23.7525-7533.1991

CaprioliRM FarmerTB GileJ. 1997. Molecular imaging of biological samples: localization of peptides and proteins using MALDI-TOF MS. Anal. Chem. 69:4751–4760.

CarbonnelleE. 2012. Robustness of two MALDI-TOF mass spectrometry systems for bacterial identification. J. Microbiol. Methods 89:133–136.

ChallisGL. 2008. Genome mining for novel natural product discovery. J. Med. Chem. 51:2618–2628.

ChaurandP StoeckliM CaprioliRM. 1999. Direct profiling of proteins in biological tissue sections by MALDI mass spectrometry. Anal. Chem. 71:5263–5270.

ClaesenJ BibbM. 2010. Genome mining and genetic analysis of cypemycin biosynthesis reveal an unusual class of posttranslationally modified peptides. Proc. Natl. Acad. Sci. U. S. A. 107:16297–16302.

de JongA van HeelAJ KokJ KuipersOP. 2010. BAGEL2: mining for bacteriocins in genomic data. Nucleic Acids Res. 38:W647–W651.

EdwardsJR HayashiJA. 1965. Structure of a rhamnolipid from Pseudomonas aeruginosa. Arch. Biochem. Biophys. 111:415–421.

GonzalezDJ. 2011. Microbial competition between Bacillus subtilis and Staphylococcus aureus monitored by imaging mass spectrometry. Microbiology 157:2485–2492.

GoulitquerS PotinP TononT. 2012. Mass spectrometry-based metabolomics to elucidate functions in marine organisms and ecosystems. Mar. Drugs 10:849–880.

GustafssonJO OehlerMK RuszkiewiczA McCollSR HoffmannP. 2011. MALDI imaging mass spectrometry (MALDI-IMS)—application of spatial proteomics for ovarian cancer classification and diagnosis. Int. J. Mol. Sci. 12:773–794.

HankinJA BarkleyRM MurphyRC. 2007. Sublimation as a method of matrix application for mass spectrometric imaging. J. Am. Soc. Mass Spectrom. 18:1646–1652.

HisatsukaK NakaharaT MinodaT YamadaK. 1971. Formation of rhamnolipid by Pseudomonas aeruginosa and its function in hydrocarbon fermentation. Agric. Biol. Chem. 35:686–692.

HoraiH. 2010. MassBank: a public repository for sharing mass spectral data for life sciences. J. Mass. Spectrom. 45:703–714.

HufskyF RemptM RascheF PohnertG BöckerS. 2012. De novo analysis of electron impact mass spectra using fragmentation trees. Anal. Chim. Acta 739:67–76.

IbanezAJ MuckA SvatosA. 2007. Dissipation of charge on MALDI-TOF polymeric chips using an electron-acceptor: analysis of proteins. J. Mass Spectrom. 42:634–640.

InagawaH. 1992. Homeostasis as regulated by activated macrophage. II. LPS of plant origin other than wheat flour and their concomitant bacteria. Chem. Pharm. Bull. (Tokyo) 40:994–997.

ItohS HondaH TomitaF SuzukiT. 1971. Rhamnolipid produced by Pseudomonas aeruginosa grown on n-paraffin. J. Antibiot. 24:855–859.

Jardin-MatheO. 2008. MITICS (MALDI Imaging Team Imaging Computing System): a new open source mass spectrometry imaging software. J. Proteomics 71:332–345.

10.1128/jb.95.2.732-733.1968

10.1038/nrmicro2405

KerstenRD. 2011. A mass spectrometry-guided genome mining approach for natural product peptidogenomics. Nat. Chem. Biol. 7:794–802.

KimS BandieraN PevznerPA. 2009. Spectral profiles, a novel representation of tandem mass spectra and their applications for de novo peptide sequencing and identification. Mol. Cell. Proteomics 8:1391–1400.

LiMH UngPM ZajkowskiJ Garneau-TsodikovaS ShermanDH. 2009. Automated genome mining for natural products. BMC Bioinformatics 10:185.

LiuW-T. 2010. Imaging mass spectrometry of intraspecies metabolic exchange revealed the cannibalistic factors of Bacillus subtilis. Proc. Natl. Acad. Sci. U. S. A. 107:16286–16290.

LopezD KolterR. 2010. Extracellular signals that define distinct and coexisting cell fates in Bacillus subtilis. FEMS Microbiol. Rev. 34:134–149.

LoweryCA DickersonTJ JandaKD. 2008. Interspecies and interkingdom communication mediated by bacterial quorum sensing. Chem. Soc. Rev. 37:1337–1346.

MackeySR GoldenSS DittyJL. 2011. The itty-bitty time machine genetics of the cyanobacterial circadian clock. Adv. Genet. 74:13–53.

MatsuyamaT SogawaM NakagawaY. 1989. Fractal spreading growth of Serratia marcescens which produces surface active exolipids. FEMS Microbiol. Lett. 52:243–246.

10.1128/jb.174.6.1769-1776.1992

10.1093/nar/gkr466

10.1146/annurev.micro.55.1.165

PadliyaND WoodTD. 2004. A strategy to improve peptide mass fingerprinting matches through the optimization of matrix-assisted laser desorption/ionization matrix selection and formulation. Proteomics 4:466–473.

PuolitaivalSM BurnumKE CornettDS CaprioliRM. 2008. Solvent-free matrix dry-coating for MALDI imaging of phospholipids. J. Am. Soc. Mass Spectrom. 19:882–886.

RatcliffWC DenisonRF. 2011. Alternative actions for antibiotics. Science 332:547–548.

RauschC WeberT KohlbacherO WohllebenW HusonDH. 2005. Specificity prediction of adenylation domains in nonribosomal peptide synthetases (NRPS) using transductive support vector machines (TSVMs). Nucleic Acids Res. 33:5799–5808.

Rojas-ChertoM. 2012. Metabolite identification using automated comparison of high-resolution multistage mass spectral trees. Anal. Chem. 84:5524–5534.

10.1021/cr2000509

RöttigM. 2011. NRPSpredictor2—a web server for predicting NRPS adenylation domain specificity. Nucleic Acids Res. 39:W362–W367.

10.1128/JCM.01890-10

SeeleyEH CaprioliRM. 2011. MALDI imaging mass spectrometry of human tissue: method challenges and clinical perspectives. Trends Biotechnol. 29:136–143.

ShankEA KolterR. 2011. Extracellular signaling and multicellularity in Bacillus subtilis. Curr. Opin. Microbiol. 14:741–747.

SmithCA. 2005. METLIN: a metabolite mass spectral database. Ther. Drug Monit. 27:747–751.

SogawaK. 2011. Use of the MALDI BioTyper system with MALDI-TOF mass spectrometry for rapid identification of microorganisms. Anal. Bioanal. Chem. 400:1905–1911.

StackebrandtE GoebelBM. 1994. Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int. J. Syst. Evol. Microbiol. 44:846–849.

10.1093/nar/gkn685

SteinhauserML. 2012. Multi-isotope imaging mass spectrometry quantifies stem cell division and metabolism. Nature 481:516–519.

StoeckliM FarmerTB CaprioliRM. 1999. Automated mass spectrometry imaging with a matrix-assisted laser desorption ionization time-of-flight instrument. J. Am. Soc. Mass Spectrom. 10:67–71.

StoeckliM ChaurandP HallahanDE CaprioliRM. 2001. Imaging mass spectrometry: a new technology for the analysis of protein expression in mammalian tissues. Nat. Med. 7:493–496.

10.1128/JB.00162-06

10.1146/annurev.micro.091208.073248

SwiftS. 2001. Quorum sensing as a population-density-dependent determinant of bacterial physiology. Adv. Microb. Physiol. 45:199–270.

TaeH KongEB ParkK. 2007. ASMPKS: an analysis system for modular polyketide synthases. BMC Bioinformatics 8:327.

VelasquezJE van der DonkWA. 2011. Genome mining for ribosomally synthesized natural products. Curr. Opin. Chem. Biol. 15:11–21.

10.1038/nrmicro2634

WeberT. 2009. CLUSEAN: a computer-based framework for the automated analysis of bacterial secondary metabolite biosynthetic gene clusters. J. Biotechnol. 140:13–17.

WernerHW MorganAE. 1976. Charging of insulators by ion bombardment and its minimization for secondary ion mass spectrometry (SIMS) measurement. J. Appl. Phys. 47:1232–1242.

XuY. 2012. Bacterial biosynthesis and maturation of the didemnin anti-cancer agents. J. Am. Chem. Soc. 134:8625–8632.

YadavG GokhaleRS MohantyD. 2003. SEARCHPKS: a program for detection and analysis of polyketide synthase domains. Nucleic Acid Res. 31:3654–3658.

10.1002/anie.201101225

10.1038/nchembio.252

ZhangD-S. 2012. Multi-isotope imaging mass spectrometry reveals slow protein turnover in hair-cell stereocilia. Nature 481:520–524.

Thông tin
Thông tin xuất bản

Journal of Bacteriology

Tập 194 Số 22

6023-6028

Thông tin tác giả