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Identification, cloning and characterization of SpEX exotoxin produced by Staphylococcus pseudintermedius.

Abouelkhair MA, Bemis DA, Giannone RJ, Frank LA, Kania SA.

PLoS One. 2019 Jul 29;14(7):e0220301. doi: 10.1371/journal.pone.0220301. eCollection 2019.


Effects of microbiota-directed foods in gnotobiotic animals and undernourished children.

Gehrig JL, Venkatesh S, Chang HW, Hibberd MC, Kung VL, Cheng J, Chen RY, Subramanian S, Cowardin CA, Meier MF, O'Donnell D, Talcott M, Spears LD, Semenkovich CF, Henrissat B, Giannone RJ, Hettich RL, Ilkayeva O, Muehlbauer M, Newgard CB, Sawyer C, Head RD, Rodionov DA, Arzamasov AA, Leyn SA, Osterman AL, Hossain MI, Islam M, Choudhury N, Sarker SA, Huq S, Mahmud I, Mostafa I, Mahfuz M, Barratt MJ, Ahmed T, Gordon JI.

Science. 2019 Jul 12;365(6449). pii: eaau4732. doi: 10.1126/science.aau4732.


Exploiting the Dynamic Relationship between Peptide Separation Quality and Peptide Coisolation in a Multiple-Peptide Matches-per-Spectrum Approach Offers a Strategy To Optimize Bottom-Up Proteomics Throughput and Depth.

Villalobos Solis MI, Giannone RJ, Hettich RL, Abraham PE.

Anal Chem. 2019 Jun 4;91(11):7273-7279. doi: 10.1021/acs.analchem.9b00819. Epub 2019 May 22.


Expression of benzoyl-CoA metabolism genes in the lignocellulolytic host Caldicellulosiruptor bescii.

Sander K, Yeary M, Mahan K, Whitham J, Giannone RJ, Brown SD, Rodriguez M Jr, Graham DE, Hankoua B.

AMB Express. 2019 May 4;9(1):59. doi: 10.1186/s13568-019-0783-8.


Scavenging organic nitrogen and remodelling lipid metabolism are key survival strategies adopted by the endophytic fungi, Serendipita vermifera and Serendipita bescii to alleviate nitrogen and phosphorous starvation in vitro.

Ray P, Abraham PE, Guo Y, Giannone RJ, Engle NL, Yang ZK, Jacobson D, Hettich RL, Tschaplinski TJ, Craven KD.

Environ Microbiol Rep. 2019 Aug;11(4):548-557. doi: 10.1111/1758-2229.12757. Epub 2019 May 1.


Evaluation of an untargeted nano-liquid chromatography-mass spectrometry approach to expand coverage of low molecular weight dissolved organic matter in Arctic soil.

Ladd MP, Giannone RJ, Abraham PE, Wullschleger SD, Hettich RL.

Sci Rep. 2019 Apr 9;9(1):5810. doi: 10.1038/s41598-019-42118-9.


Characterization of a leukocidin identified in Staphylococcus pseudintermedius.

Abouelkhair MA, Bemis DA, Giannone RJ, Frank LA, Kania SA.

PLoS One. 2018 Sep 27;13(9):e0204450. doi: 10.1371/journal.pone.0204450. eCollection 2018.


Rapid, Parallel Identification of Catabolism Pathways of Lignin-Derived Aromatic Compounds in Novosphingobium aromaticivorans.

Cecil JH, Garcia DC, Giannone RJ, Michener JK.

Appl Environ Microbiol. 2018 Oct 30;84(22). pii: e01185-18. doi: 10.1128/AEM.01185-18. Print 2018 Nov 15.


Transcriptomic and proteomic changes from medium supplementation and strain evolution in high-yielding Clostridium thermocellum strains.

Papanek B, O'Dell KB, Manga P, Giannone RJ, Klingeman DM, Hettich RL, Brown SD, Guss AM.

J Ind Microbiol Biotechnol. 2018 Nov;45(11):1007-1015. doi: 10.1007/s10295-018-2073-x. Epub 2018 Sep 5.


Identification of parallel and divergent optimization solutions for homologous metabolic enzymes.

Standaert RF, Giannone RJ, Michener JK.

Metab Eng Commun. 2018 Apr 18;6:56-62. doi: 10.1016/j.meteno.2018.04.002. eCollection 2018 Jun.


The diversity and specificity of the extracellular proteome in the cellulolytic bacterium Caldicellulosiruptor bescii is driven by the nature of the cellulosic growth substrate.

Poudel S, Giannone RJ, Basen M, Nookaew I, Poole FL 2nd, Kelly RM, Adams MWW, Hettich RL.

Biotechnol Biofuels. 2018 Mar 23;11:80. doi: 10.1186/s13068-018-1076-1. eCollection 2018.


Insights into the Evolution of Host Association through the Isolation and Characterization of a Novel Human Periodontal Pathobiont, Desulfobulbus oralis.

Cross KL, Chirania P, Xiong W, Beall CJ, Elkins JG, Giannone RJ, Griffen AL, Guss AM, Hettich RL, Joshi SS, Mokrzan EM, Martin RK, Zhulin IB, Leys EJ, Podar M.

MBio. 2018 Mar 13;9(2). pii: e02061-17. doi: 10.1128/mBio.02061-17.


Deletion of the hfsB gene increases ethanol production in Thermoanaerobacterium saccharolyticum and several other thermophilic anaerobic bacteria.

Eminoğlu A, Murphy SJ, Maloney M, Lanahan A, Giannone RJ, Hettich RL, Tripathi SA, Beldüz AO, Lynd LR, Olson DG.

Biotechnol Biofuels. 2017 Nov 30;10:282. doi: 10.1186/s13068-017-0968-9. eCollection 2017.


Functional Analysis of the Glucan Degradation Locus in Caldicellulosiruptor bescii Reveals Essential Roles of Component Glycoside Hydrolases in Plant Biomass Deconstruction.

Conway JM, McKinley BS, Seals NL, Hernandez D, Khatibi PA, Poudel S, Giannone RJ, Hettich RL, Williams-Rhaesa AM, Lipscomb GL, Adams MWW, Kelly RM.

Appl Environ Microbiol. 2017 Dec 1;83(24). pii: e01828-17. doi: 10.1128/AEM.01828-17. Print 2017 Dec 15.


Molecular basis of surface anchored protein A deficiency in the Staphylococcus aureus strain Wood 46.

Balachandran M, Giannone RJ, Bemis DA, Kania SA.

PLoS One. 2017 Aug 31;12(8):e0183913. doi: 10.1371/journal.pone.0183913. eCollection 2017.


Corrigendum: Pentose sugars inhibit metabolism and increase expression of an AgrD-type cyclic pentapeptide in Clostridium thermocellum.

Verbeke TJ, Giannone RJ, Klingeman DM, Engle NL, Rydzak T, Guss AM, Tschaplinski TJ, Brown SD, Hettich RL, Elkins JG.

Sci Rep. 2017 Jul 27;7:46875. doi: 10.1038/srep46875.


Construction and Optimization of a Heterologous Pathway for Protocatechuate Catabolism in Escherichia coli Enables Bioconversion of Model Aromatic Compounds.

Clarkson SM, Giannone RJ, Kridelbaugh DM, Elkins JG, Guss AM, Michener JK.

Appl Environ Microbiol. 2017 Aug 31;83(18). pii: e01313-17. doi: 10.1128/AEM.01313-17. Print 2017 Sep 15.


Multi-omics analysis provides insight to the Ignicoccus hospitalis-Nanoarchaeum equitans association.

Rawle RA, Hamerly T, Tripet BP, Giannone RJ, Wurch L, Hettich RL, Podar M, Copié V, Bothner B.

Biochim Biophys Acta Gen Subj. 2017 Sep;1861(9):2218-2227. doi: 10.1016/j.bbagen.2017.06.001. Epub 2017 Jun 4.


The effects of micronutrient deficiencies on bacterial species from the human gut microbiota.

Hibberd MC, Wu M, Rodionov DA, Li X, Cheng J, Griffin NW, Barratt MJ, Giannone RJ, Hettich RL, Osterman AL, Gordon JI.

Sci Transl Med. 2017 May 17;9(390). pii: eaal4069. doi: 10.1126/scitranslmed.aal4069.


Specialized activities and expression differences for Clostridium thermocellum biofilm and planktonic cells.

Dumitrache A, Klingeman DM, Natzke J, Rodriguez M Jr, Giannone RJ, Hettich RL, Davison BH, Brown SD.

Sci Rep. 2017 Feb 27;7:43583. doi: 10.1038/srep43583.


Pentose sugars inhibit metabolism and increase expression of an AgrD-type cyclic pentapeptide in Clostridium thermocellum.

Verbeke TJ, Giannone RJ, Klingeman DM, Engle NL, Rydzak T, Guss AM, Tschaplinski TJ, Brown SD, Hettich RL, Elkins JG.

Sci Rep. 2017 Feb 23;7:43355. doi: 10.1038/srep43355. Erratum in: Sci Rep. 2017 Jul 27;7:46875.


Integrated omics analyses reveal the details of metabolic adaptation of Clostridium thermocellum to lignocellulose-derived growth inhibitors released during the deconstruction of switchgrass.

Poudel S, Giannone RJ, Rodriguez M Jr, Raman B, Martin MZ, Engle NL, Mielenz JR, Nookaew I, Brown SD, Tschaplinski TJ, Ussery D, Hettich RL.

Biotechnol Biofuels. 2017 Jan 10;10:14. doi: 10.1186/s13068-016-0697-5. eCollection 2017.


Improved growth rate in Clostridium thermocellum hydrogenase mutant via perturbed sulfur metabolism.

Biswas R, Wilson CM, Giannone RJ, Klingeman DM, Rydzak T, Shah MB, Hettich RL, Brown SD, Guss AM.

Biotechnol Biofuels. 2017 Jan 3;10:6. doi: 10.1186/s13068-016-0684-x. eCollection 2017.


Transcriptomic and proteomic insights into innate immunity and adaptations to a symbiotic lifestyle in the gutless marine worm Olavius algarvensis.

Wippler J, Kleiner M, Lott C, Gruhl A, Abraham PE, Giannone RJ, Young JC, Hettich RL, Dubilier N.

BMC Genomics. 2016 Nov 21;17(1):942.


Genomics-informed isolation and characterization of a symbiotic Nanoarchaeota system from a terrestrial geothermal environment.

Wurch L, Giannone RJ, Belisle BS, Swift C, Utturkar S, Hettich RL, Reysenbach AL, Podar M.

Nat Commun. 2016 Jul 5;7:12115. doi: 10.1038/ncomms12115.


Simultaneous achievement of high ethanol yield and titer in Clostridium thermocellum.

Tian L, Papanek B, Olson DG, Rydzak T, Holwerda EK, Zheng T, Zhou J, Maloney M, Jiang N, Giannone RJ, Hettich RL, Guss AM, Lynd LR.

Biotechnol Biofuels. 2016 Jun 2;9:116. doi: 10.1186/s13068-016-0528-8. eCollection 2016.


Development of a plasmid-based expression system in Clostridium thermocellum and its use to screen heterologous expression of bifunctional alcohol dehydrogenases (adhEs).

Hon S, Lanahan AA, Tian L, Giannone RJ, Hettich RL, Olson DG, Lynd LR.

Metab Eng Commun. 2016 Apr 22;3:120-129. doi: 10.1016/j.meteno.2016.04.001. eCollection 2016 Dec.


Dramatic performance of Clostridium thermocellum explained by its wide range of cellulase modalities.

Xu Q, Resch MG, Podkaminer K, Yang S, Baker JO, Donohoe BS, Wilson C, Klingeman DM, Olson DG, Decker SR, Giannone RJ, Hettich RL, Brown SD, Lynd LR, Bayer EA, Himmel ME, Bomble YJ.

Sci Adv. 2016 Feb 5;2(2):e1501254. doi: 10.1126/sciadv.1501254. eCollection 2016 Feb.


Untargeted metabolomics studies employing NMR and LC-MS reveal metabolic coupling between Nanoarcheum equitans and its archaeal host Ignicoccus hospitalis.

Hamerly T, Tripet BP, Tigges M, Giannone RJ, Wurch L, Hettich RL, Podar M, Copié V, Bothner B.

Metabolomics. 2015 Aug 1;11(4):895-907.


Rescuing Those Left Behind: Recovering and Characterizing Underdigested Membrane and Hydrophobic Proteins To Enhance Proteome Measurement Depth.

Giannone RJ, Wurch LL, Podar M, Hettich RL.

Anal Chem. 2015 Aug 4;87(15):7720-8. doi: 10.1021/acs.analchem.5b01187. Epub 2015 Jul 21.


Discrete and structurally unique proteins (tāpirins) mediate attachment of extremely thermophilic Caldicellulosiruptor species to cellulose.

Blumer-Schuette SE, Alahuhta M, Conway JM, Lee LL, Zurawski JV, Giannone RJ, Hettich RL, Lunin VV, Himmel ME, Kelly RM.

J Biol Chem. 2015 Apr 24;290(17):10645-56. doi: 10.1074/jbc.M115.641480. Epub 2015 Feb 26.


A comparative multidimensional LC-MS proteomic analysis reveals mechanisms for furan aldehyde detoxification in Thermoanaerobacter pseudethanolicus 39E.

Clarkson SM, Hamilton-Brehm SD, Giannone RJ, Engle NL, Tschaplinski TJ, Hettich RL, Elkins JG.

Biotechnol Biofuels. 2014 Dec 3;7(1):165. doi: 10.1186/s13068-014-0165-z. eCollection 2014.


Development of an enhanced metaproteomic approach for deepening the microbiome characterization of the human infant gut.

Xiong W, Giannone RJ, Morowitz MJ, Banfield JF, Hettich RL.

J Proteome Res. 2015 Jan 2;14(1):133-41. doi: 10.1021/pr500936p. Epub 2014 Nov 12.


Life on the edge: functional genomic response of Ignicoccus hospitalis to the presence of Nanoarchaeum equitans.

Giannone RJ, Wurch LL, Heimerl T, Martin S, Yang Z, Huber H, Rachel R, Hettich RL, Podar M.

ISME J. 2015 Jan;9(1):101-14. doi: 10.1038/ismej.2014.112. Epub 2014 Jul 11.


Metaproteomics: extracting and mining proteome information to characterize metabolic activities in microbial communities.

Abraham PE, Giannone RJ, Xiong W, Hettich RL.

Curr Protoc Bioinformatics. 2014 Jun 17;46:13.26.1-14. doi: 10.1002/0471250953.bi1326s46.


Profile of secreted hydrolases, associated proteins, and SlpA in Thermoanaerobacterium saccharolyticum during the degradation of hemicellulose.

Currie DH, Guss AM, Herring CD, Giannone RJ, Johnson CM, Lankford PK, Brown SD, Hettich RL, Lynd LR.

Appl Environ Microbiol. 2014 Aug;80(16):5001-11. doi: 10.1128/AEM.00998-14. Epub 2014 Jun 6.


Metaproteomics: harnessing the power of high performance mass spectrometry to identify the suite of proteins that control metabolic activities in microbial communities.

Hettich RL, Pan C, Chourey K, Giannone RJ.

Anal Chem. 2013 May 7;85(9):4203-14. doi: 10.1021/ac303053e. Epub 2013 Mar 21. Review.


Role of the CipA scaffoldin protein in cellulose solubilization, as determined by targeted gene deletion and complementation in Clostridium thermocellum.

Olson DG, Giannone RJ, Hettich RL, Lynd LR.

J Bacteriol. 2013 Feb;195(4):733-9. doi: 10.1128/JB.02014-12. Epub 2012 Nov 30.


Putting the pieces together: high-performance LC-MS/MS provides network-, pathway-, and protein-level perspectives in Populus.

Abraham P, Giannone RJ, Adams RM, Kalluri U, Tuskan GA, Hettich RL.

Mol Cell Proteomics. 2013 Jan;12(1):106-19. doi: 10.1074/mcp.M112.022996. Epub 2012 Oct 16.


Clostridium thermocellum ATCC27405 transcriptomic, metabolomic and proteomic profiles after ethanol stress.

Yang S, Giannone RJ, Dice L, Yang ZK, Engle NL, Tschaplinski TJ, Hettich RL, Brown SD.

BMC Genomics. 2012 Jul 23;13:336. doi: 10.1186/1471-2164-13-336.


Caldicellulosiruptor core and pangenomes reveal determinants for noncellulosomal thermophilic deconstruction of plant biomass.

Blumer-Schuette SE, Giannone RJ, Zurawski JV, Ozdemir I, Ma Q, Yin Y, Xu Y, Kataeva I, Poole FL 2nd, Adams MW, Hamilton-Brehm SD, Elkins JG, Larimer FW, Land ML, Hauser LJ, Cottingham RW, Hettich RL, Kelly RM.

J Bacteriol. 2012 Aug;194(15):4015-28. doi: 10.1128/JB.00266-12. Epub 2012 May 25.


Microbial metaproteomics: identifying the repertoire of proteins that microorganisms use to compete and cooperate in complex environmental communities.

Hettich RL, Sharma R, Chourey K, Giannone RJ.

Curr Opin Microbiol. 2012 Jun;15(3):373-80. doi: 10.1016/j.mib.2012.04.008. Epub 2012 May 24. Review.


The Clavibacter michiganensis subsp. michiganensis-tomato interactome reveals the perception of pathogen by the host and suggests mechanisms of infection.

Savidor A, Teper D, Gartemann KH, Eichenlaub R, Chalupowicz L, Manulis-Sasson S, Barash I, Tews H, Mayer K, Giannone RJ, Hettich RL, Sessa G.

J Proteome Res. 2012 Feb 3;11(2):736-50. doi: 10.1021/pr200646a. Epub 2011 Dec 20.


Defining the boundaries and characterizing the landscape of functional genome expression in vascular tissues of Populus using shotgun proteomics.

Abraham P, Adams R, Giannone RJ, Kalluri U, Ranjan P, Erickson B, Shah M, Tuskan GA, Hettich RL.

J Proteome Res. 2012 Jan 1;11(1):449-60. doi: 10.1021/pr200851y. Epub 2011 Nov 9.


Label-free quantitative proteomics for the extremely thermophilic bacterium Caldicellulosiruptor obsidiansis reveal distinct abundance patterns upon growth on cellobiose, crystalline cellulose, and switchgrass.

Lochner A, Giannone RJ, Keller M, Antranikian G, Graham DE, Hettich RL.

J Proteome Res. 2011 Dec 2;10(12):5302-14. doi: 10.1021/pr200536j. Epub 2011 Nov 8.


Proteomic characterization of cellular and molecular processes that enable the Nanoarchaeum equitans--Ignicoccus hospitalis relationship.

Giannone RJ, Huber H, Karpinets T, Heimerl T, Küper U, Rachel R, Keller M, Hettich RL, Podar M.

PLoS One. 2011;6(8):e22942. doi: 10.1371/journal.pone.0022942. Epub 2011 Aug 3.


Use of label-free quantitative proteomics to distinguish the secreted cellulolytic systems of Caldicellulosiruptor bescii and Caldicellulosiruptor obsidiansis.

Lochner A, Giannone RJ, Rodriguez M Jr, Shah MB, Mielenz JR, Keller M, Antranikian G, Graham DE, Hettich RL.

Appl Environ Microbiol. 2011 Jun;77(12):4042-54. doi: 10.1128/AEM.02811-10. Epub 2011 Apr 15.


Deletion of the Cel48S cellulase from Clostridium thermocellum.

Olson DG, Tripathi SA, Giannone RJ, Lo J, Caiazza NC, Hogsett DA, Hettich RL, Guss AM, Dubrovsky G, Lynd LR.

Proc Natl Acad Sci U S A. 2010 Oct 12;107(41):17727-32. doi: 10.1073/pnas.1003584107. Epub 2010 Sep 13.


The protein network surrounding the human telomere repeat binding factors TRF1, TRF2, and POT1.

Giannone RJ, McDonald HW, Hurst GB, Shen RF, Wang Y, Liu Y.

PLoS One. 2010 Aug 25;5(8):e12407. doi: 10.1371/journal.pone.0012407.


The monitoring and affinity purification of proteins using dual tags with tetracysteine motifs.

Giannone RJ, Liu Y, Wang Y.

Methods Mol Biol. 2009;544:421-38. doi: 10.1007/978-1-59745-483-4_28.


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