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Comparative Genomics and Proteomic Analysis of Assimilatory Sulfate Reduction Pathways in Anaerobic Methanotrophic Archaea.

Yu H, Susanti D, McGlynn SE, Skennerton CT, Chourey K, Iyer R, Scheller S, Tavormina PL, Hettich RL, Mukhopadhyay B, Orphan VJ.

Front Microbiol. 2018 Dec 3;9:2917. doi: 10.3389/fmicb.2018.02917. eCollection 2018.


Quantifying codon usage in signal peptides: Gene expression and amino acid usage explain apparent selection for inefficient codons.

Cope AL, Hettich RL, Gilchrist MA.

Biochim Biophys Acta Biomembr. 2018 Dec;1860(12):2479-2485. doi: 10.1016/j.bbamem.2018.09.010. Epub 2018 Sep 19.


Utilization of a Detergent-Based Method for Direct Microbial Cellular Lysis/Proteome Extraction from Soil Samples for Metaproteomics Studies.

Chourey K, Hettich RL.

Methods Mol Biol. 2018;1841:293-302. doi: 10.1007/978-1-4939-8695-8_20.


Biogeochemical Cycling by a Low-Diversity Microbial Community in Deep Groundwater.

Bell E, Lamminmäki T, Alneberg J, Andersson AF, Qian C, Xiong W, Hettich RL, Balmer L, Frutschi M, Sommer G, Bernier-Latmani R.

Front Microbiol. 2018 Sep 7;9:2129. doi: 10.3389/fmicb.2018.02129. eCollection 2018.


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.


Diel rewiring and positive selection of ancient plant proteins enabled evolution of CAM photosynthesis in Agave.

Yin H, Guo HB, Weston DJ, Borland AM, Ranjan P, Abraham PE, Jawdy SS, Wachira J, Tuskan GA, Tschaplinski TJ, Wullschleger SD, Guo H, Hettich RL, Gross SM, Wang Z, Visel A, Yang X.

BMC Genomics. 2018 Aug 6;19(1):588. doi: 10.1186/s12864-018-4964-7.


Author Correction: Maternal consumption of fish oil programs reduced adiposity in broiler chicks.

Beckford RC, Howard SJ, Das S, Farmer AT, Campagna SR, Yu J, Hettich RL, Wilson JL, Voy BH.

Sci Rep. 2018 Jul 27;8(1):11578. doi: 10.1038/s41598-018-29512-5.


Quantitative Proteomic Analysis of Biological Processes and Responses of the Bacterium Desulfovibrio desulfuricans ND132 upon Deletion of Its Mercury Methylation Genes.

Qian C, Chen H, Johs A, Lu X, An J, Pierce EM, Parks JM, Elias DA, Hettich RL, Gu B.

Proteomics. 2018 Sep;18(17):e1700479. doi: 10.1002/pmic.201700479. Epub 2018 Aug 16.


Hospitalized Premature Infants Are Colonized by Related Bacterial Strains with Distinct Proteomic Profiles.

Brown CT, Xiong W, Olm MR, Thomas BC, Baker R, Firek B, Morowitz MJ, Hettich RL, Banfield JF.

MBio. 2018 Apr 10;9(2). pii: e00441-18. doi: 10.1128/mBio.00441-18.


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.


Quantitative proteome profile of water deficit stress responses in eastern cottonwood (Populus deltoides) leaves.

Abraham PE, Garcia BJ, Gunter LE, Jawdy SS, Engle N, Yang X, Jacobson DA, Hettich RL, Tuskan GA, Tschaplinski TJ.

PLoS One. 2018 Feb 15;13(2):e0190019. doi: 10.1371/journal.pone.0190019. eCollection 2018.


Phosphorylation of Ribosomal Protein RPS6 Integrates Light Signals and Circadian Clock Signals.

Enganti R, Cho SK, Toperzer JD, Urquidi-Camacho RA, Cakir OS, Ray AP, Abraham PE, Hettich RL, von Arnim AG.

Front Plant Sci. 2018 Jan 19;8:2210. doi: 10.3389/fpls.2017.02210. eCollection 2017.


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.


The Kalanchoë genome provides insights into convergent evolution and building blocks of crassulacean acid metabolism.

Yang X, Hu R, Yin H, Jenkins J, Shu S, Tang H, Liu D, Weighill DA, Cheol Yim W, Ha J, Heyduk K, Goodstein DM, Guo HB, Moseley RC, Fitzek E, Jawdy S, Zhang Z, Xie M, Hartwell J, Grimwood J, Abraham PE, Mewalal R, Beltrán JD, Boxall SF, Dever LV, Palla KJ, Albion R, Garcia T, Mayer JA, Don Lim S, Man Wai C, Peluso P, Van Buren R, De Paoli HC, Borland AM, Guo H, Chen JG, Muchero W, Yin Y, Jacobson DA, Tschaplinski TJ, Hettich RL, Ming R, Winter K, Leebens-Mack JH, Smith JAC, Cushman JC, Schmutz J, Tuskan GA.

Nat Commun. 2017 Dec 1;8(1):1899. doi: 10.1038/s41467-017-01491-7.


Eliminating a global regulator of carbon catabolite repression enhances the conversion of aromatic lignin monomers to muconate in Pseudomonas putida KT2440.

Johnson CW, Abraham PE, Linger JG, Khanna P, Hettich RL, Beckham GT.

Metab Eng Commun. 2017 May 31;5:19-25. doi: 10.1016/j.meteno.2017.05.002. eCollection 2017 Dec.


Maternal consumption of fish oil programs reduced adiposity in broiler chicks.

Beckford RC, Howard SJ, Das S, Farmer AT, Campagna SR, Yu J, Hettich RL, Wilson JL, Voy BH.

Sci Rep. 2017 Oct 13;7(1):13129. doi: 10.1038/s41598-017-13519-5. Erratum in: Sci Rep. 2018 Jul 27;8(1):11578.


Identification of peptide-binding sites within BSA using rapid, laser-induced covalent cross-linking combined with high-performance mass spectrometry.

Hauser M, Qian C, King ST, Kauffman S, Naider F, Hettich RL, Becker JM.

J Mol Recognit. 2018 Feb;31(2). doi: 10.1002/jmr.2680. Epub 2017 Oct 10.


Functional analysis of the Glucan Degradation Locus (GDL) 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 Oct 6. pii: AEM.01828-17. doi: 10.1128/AEM.01828-17. [Epub ahead of print]


Erratum for Skennerton et al., "Methane-Fueled Syntrophy through Extracellular Electron Transfer: Uncovering the Genomic Traits Conserved within Diverse Bacterial Partners of Anaerobic Methanotrophic Archaea".

Skennerton CT, Chourey K, Iyer R, Hettich RL, Tyson GW, Orphan VJ.

MBio. 2017 Oct 3;8(5). pii: e01561-17. doi: 10.1128/mBio.01561-17. No abstract available.


Mechanisms of subzero growth in the cryophile Planococcus halocryophilus determined through proteomic analysis.

Raymond-Bouchard I, Chourey K, Altshuler I, Iyer R, Hettich RL, Whyte LG.

Environ Microbiol. 2017 Nov;19(11):4460-4479. doi: 10.1111/1462-2920.13893. Epub 2017 Oct 13.


Grape pomace compost harbors organohalide-respiring Dehalogenimonas species with novel reductive dehalogenase genes.

Yang Y, Higgins SA, Yan J, Şimşir B, Chourey K, Iyer R, Hettich RL, Baldwin B, Ogles DM, Löffler FE.

ISME J. 2017 Dec;11(12):2767-2780. doi: 10.1038/ismej.2017.127. Epub 2017 Aug 15.


Phylogenetically conserved resource partitioning in the coastal microbial loop.

Bryson S, Li Z, Chavez F, Weber PK, Pett-Ridge J, Hettich RL, Pan C, Mayali X, Mueller RS.

ISME J. 2017 Dec;11(12):2781-2792. doi: 10.1038/ismej.2017.128. Epub 2017 Aug 11.


Methane-Fueled Syntrophy through Extracellular Electron Transfer: Uncovering the Genomic Traits Conserved within Diverse Bacterial Partners of Anaerobic Methanotrophic Archaea.

Skennerton CT, Chourey K, Iyer R, Hettich RL, Tyson GW, Orphan VJ.

MBio. 2017 Aug 1;8(4). pii: e00530-17. doi: 10.1128/mBio.00530-17. Erratum in: MBio. 2017 Oct 3;8(5):.


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.


Genome-resolved metaproteomic characterization of preterm infant gut microbiota development reveals species-specific metabolic shifts and variabilities during early life.

Xiong W, Brown CT, Morowitz MJ, Banfield JF, Hettich RL.

Microbiome. 2017 Jul 10;5(1):72. doi: 10.1186/s40168-017-0290-6.


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.


Optimized Extraction Method To Remove Humic Acid Interferences from Soil Samples Prior to Microbial Proteome Measurements.

Qian C, Hettich RL.

J Proteome Res. 2017 Jul 7;16(7):2537-2546. doi: 10.1021/acs.jproteome.7b00103. Epub 2017 Jun 5.


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.


Genome-Resolved Meta-Omics Ties Microbial Dynamics to Process Performance in Biotechnology for Thiocyanate Degradation.

Kantor RS, Huddy RJ, Iyer R, Thomas BC, Brown CT, Anantharaman K, Tringe S, Hettich RL, Harrison ST, Banfield JF.

Environ Sci Technol. 2017 Mar 7;51(5):2944-2953. doi: 10.1021/acs.est.6b04477. Epub 2017 Feb 13.


The protein and neutral lipid composition of lipid droplets isolated from the fission yeast, Schizosaccharomyces pombe.

Meyers A, Chourey K, Weiskittel TM, Pfiffner S, Dunlap JR, Hettich RL, Dalhaimer P.

J Microbiol. 2017 Feb;55(2):112-122. doi: 10.1007/s12275-017-6205-1. Epub 2017 Jan 26.


Impacts of chemical gradients on microbial community structure.

Chen J, Hanke A, Tegetmeyer HE, Kattelmann I, Sharma R, Hamann E, Hargesheimer T, Kraft B, Lenk S, Geelhoed JS, Hettich RL, Strous M.

ISME J. 2017 Apr;11(4):920-931. doi: 10.1038/ismej.2016.175. Epub 2017 Jan 17.


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.


Transcript, protein and metabolite temporal dynamics in the CAM plant Agave.

Abraham PE, Yin H, Borland AM, Weighill D, Lim SD, De Paoli HC, Engle N, Jones PC, Agh R, Weston DJ, Wullschleger SD, Tschaplinski T, Jacobson D, Cushman JC, Hettich RL, Tuskan GA, Yang X.

Nat Plants. 2016 Nov 21;2:16178. doi: 10.1038/nplants.2016.178.


Proteogenomic analyses indicate bacterial methylotrophy and archaeal heterotrophy are prevalent below the grass root zone.

Butterfield CN, Li Z, Andeer PF, Spaulding S, Thomas BC, Singh A, Hettich RL, Suttle KB, Probst AJ, Tringe SG, Northen T, Pan C, Banfield JF.

PeerJ. 2016 Nov 8;4:e2687. eCollection 2016.


Proteomic Stable Isotope Probing Reveals Taxonomically Distinct Patterns in Amino Acid Assimilation by Coastal Marine Bacterioplankton.

Bryson S, Li Z, Pett-Ridge J, Hettich RL, Mayali X, Pan C, Mueller RS.

mSystems. 2016 Apr 26;1(2). pii: e00027-15. eCollection 2016 Mar-Apr.


Reconstructing a hydrogen-driven microbial metabolic network in Opalinus Clay rock.

Bagnoud A, Chourey K, Hettich RL, de Bruijn I, Andersson AF, Leupin OX, Schwyn B, Bernier-Latmani R.

Nat Commun. 2016 Oct 14;7:12770. doi: 10.1038/ncomms12770.


Global Proteome Response to Deletion of Genes Related to Mercury Methylation and Dissimilatory Metal Reduction Reveals Changes in Respiratory Metabolism in Geobacter sulfurreducens PCA.

Qian C, Johs A, Chen H, Mann BF, Lu X, Abraham PE, Hettich RL, Gu B.

J Proteome Res. 2016 Oct 7;15(10):3540-3549. Epub 2016 Sep 2.


Metabolic Regulation as a Consequence of Anaerobic 5-Methylthioadenosine Recycling in Rhodospirillum rubrum.

North JA, Sriram J, Chourey K, Ecker CD, Sharma R, Wildenthal JA, Hettich RL, Tabita FR.

MBio. 2016 Jul 12;7(4). pii: e00855-16. doi: 10.1128/mBio.00855-16.


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.


Proteomic Stable Isotope Probing Reveals Biosynthesis Dynamics of Slow Growing Methane Based Microbial Communities.

Marlow JJ, Skennerton CT, Li Z, Chourey K, Hettich RL, Pan C, Orphan VJ.

Front Microbiol. 2016 Apr 29;7:563. doi: 10.3389/fmicb.2016.00563. 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.


Fungi Contribute Critical but Spatially Varying Roles in Nitrogen and Carbon Cycling in Acid Mine Drainage.

Mosier AC, Miller CS, Frischkorn KR, Ohm RA, Li Z, LaButti K, Lapidus A, Lipzen A, Chen C, Johnson J, Lindquist EA, Pan C, Hettich RL, Grigoriev IV, Singer SW, Banfield JF.

Front Microbiol. 2016 Mar 3;7:238. doi: 10.3389/fmicb.2016.00238. eCollection 2016.


Characterization of Fatty Acids in Crenarchaeota by GC-MS and NMR.

Hamerly T, Tripet B, Wurch L, Hettich RL, Podar M, Bothner B, Copié V.

Archaea. 2015 Dec 31;2015:472726. doi: 10.1155/2015/472726. eCollection 2015.

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