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The streptothricin acetyltransferase (sat) gene as a positive selectable marker for methanogenic archaea.

Farley KR, Metcalf WW.

FEMS Microbiol Lett. 2019 Sep 1;366(17). pii: fnz216. doi: 10.1093/femsle/fnz216.


GDGT cyclization proteins identify the dominant archaeal sources of tetraether lipids in the ocean.

Zeng Z, Liu XL, Farley KR, Wei JH, Metcalf WW, Summons RE, Welander PV.

Proc Natl Acad Sci U S A. 2019 Nov 5;116(45):22505-22511. doi: 10.1073/pnas.1909306116. Epub 2019 Oct 7.


Energy Conservation and Hydrogenase Function in Methanogenic Archaea, in Particular the Genus Methanosarcina.

Mand TD, Metcalf WW.

Microbiol Mol Biol Rev. 2019 Sep 18;83(4). pii: e00020-19. doi: 10.1128/MMBR.00020-19. Print 2019 Nov 20. Review.


Fosmidomycin biosynthesis diverges from related phosphonate natural products.

Parkinson EI, Erb A, Eliot AC, Ju KS, Metcalf WW.

Nat Chem Biol. 2019 Nov;15(11):1049-1056. doi: 10.1038/s41589-019-0343-1. Epub 2019 Aug 26.


GWAS and PheWAS of red blood cell components in a Northern Nevadan cohort.

Read RW, Schlauch KA, Elhanan G, Metcalf WJ, Slonim AD, Aweti R, Borkowski R, Grzymski JJ.

PLoS One. 2019 Jun 13;14(6):e0218078. doi: 10.1371/journal.pone.0218078. eCollection 2019.


Methylamine-specific methyltransferase paralogs in Methanosarcina are functionally distinct despite frequent gene conversion.

Nayak DD, Metcalf WW.

ISME J. 2019 Sep;13(9):2173-2182. doi: 10.1038/s41396-019-0428-6. Epub 2019 May 3.


Biochemical Characterization of the Methylmercaptopropionate:Cob(I)alamin Methyltransferase from Methanosarcina acetivorans.

Fu H, Goettge MN, Metcalf WW.

J Bacteriol. 2019 May 22;201(12). pii: e00130-19. doi: 10.1128/JB.00130-19. Print 2019 Jun 15.


Molecular Basis of Bacillus subtilis ATCC 6633 Self-Resistance to the Phosphono-oligopeptide Antibiotic Rhizocticin.

Petronikolou N, Ortega MA, Borisova SA, Nair SK, Metcalf WW.

ACS Chem Biol. 2019 Apr 19;14(4):742-750. doi: 10.1021/acschembio.9b00030. Epub 2019 Mar 13.


Genetic techniques for studies of methyl-coenzyme M reductase from Methanosarcina acetivorans C2A.

Nayak DD, Metcalf WW.

Methods Enzymol. 2018;613:325-347. doi: 10.1016/bs.mie.2018.10.012. Epub 2018 Nov 23.


An assessment of true and false positive detection rates of stepwise epistatic model selection as a function of sample size and number of markers.

Chen AH, Ge W, Metcalf W, Jakobsson E, Mainzer LS, Lipka AE.

Heredity (Edinb). 2019 May;122(5):660-671. doi: 10.1038/s41437-018-0162-2. Epub 2018 Nov 15.


Genetic, Biochemical, and Molecular Characterization of Methanosarcina barkeri Mutants Lacking Three Distinct Classes of Hydrogenase.

Mand TD, Kulkarni G, Metcalf WW.

J Bacteriol. 2018 Sep 24;200(20). pii: e00342-18. doi: 10.1128/JB.00342-18. Print 2018 Oct 15.


Energy Conservation via Hydrogen Cycling in the Methanogenic Archaeon Methanosarcina barkeri.

Kulkarni G, Mand TD, Metcalf WW.

MBio. 2018 Jul 3;9(4). pii: e01256-18. doi: 10.1128/mBio.01256-18.


PcxL and HpxL are flavin-dependent, oxime-forming N-oxidases in phosphonocystoximic acid biosynthesis in Streptomyces.

Goettge MN, Cioni JP, Ju KS, Pallitsch K, Metcalf WW.

J Biol Chem. 2018 May 4;293(18):6859-6868. doi: 10.1074/jbc.RA118.001721. Epub 2018 Mar 14.


Discovery of the Tyrobetaine Natural Products and Their Biosynthetic Gene Cluster via Metabologenomics.

Parkinson EI, Tryon JH, Goering AW, Ju KS, McClure RA, Kemball JD, Zhukovsky S, Labeda DP, Thomson RJ, Kelleher NL, Metcalf WW.

ACS Chem Biol. 2018 Apr 20;13(4):1029-1037. doi: 10.1021/acschembio.7b01089. Epub 2018 Mar 13.


Draft Genome Sequence of Methanobrevibacter smithii Isolate WWM1085, Obtained from a Human Stool Sample.

Jennings ME, Chia N, Boardman LA, Metcalf WW.

Genome Announc. 2017 Sep 28;5(39). pii: e01055-17. doi: 10.1128/genomeA.01055-17.


Post-translational thioamidation of methyl-coenzyme M reductase, a key enzyme in methanogenic and methanotrophic Archaea.

Nayak DD, Mahanta N, Mitchell DA, Metcalf WW.

Elife. 2017 Sep 7;6. pii: e29218. doi: 10.7554/eLife.29218.


Classic Spotlights: Selected Highlights from the First 100 Years of the Journal of Bacteriology.

Armitage JP, Becker A, Christie PJ, de Boer PAJ, DiRita VJ, Gourse RL, Henkin TM, Margolin W, Metcalf WW, Mullineaux CW, O'Toole GA, Parkinson JS, Schneewind O, Silhavy TJ, Stock AM, Zhulin IB.

J Bacteriol. 2017 Jun 13;199(13). pii: e00062-17. doi: 10.1128/JB.00062-17. Print 2017 Jul 1. No abstract available.


Cas9-mediated genome editing in the methanogenic archaeon Methanosarcina acetivorans.

Nayak DD, Metcalf WW.

Proc Natl Acad Sci U S A. 2017 Mar 14;114(11):2976-2981. doi: 10.1073/pnas.1618596114. Epub 2017 Mar 6.


Phylogenetic relationships in the family Streptomycetaceae using multi-locus sequence analysis.

Labeda DP, Dunlap CA, Rong X, Huang Y, Doroghazi JR, Ju KS, Metcalf WW.

Antonie Van Leeuwenhoek. 2017 Apr;110(4):563-583. doi: 10.1007/s10482-016-0824-0. Epub 2016 Dec 30.


Classic Spotlight: Metabolic Flux-Which Way To Go?

Metcalf WW.

J Bacteriol. 2016 Nov 18;198(24):3248-3249. Print 2016 Dec 15. No abstract available.


Genome-wide gene expression and RNA half-life measurements allow predictions of regulation and metabolic behavior in Methanosarcina acetivorans.

Peterson JR, Thor S, Kohler L, Kohler PR, Metcalf WW, Luthey-Schulten Z.

BMC Genomics. 2016 Nov 16;17(1):924.


Elucidating the Rimosamide-Detoxin Natural Product Families and Their Biosynthesis Using Metabolite/Gene Cluster Correlations.

McClure RA, Goering AW, Ju KS, Baccile JA, Schroeder FC, Metcalf WW, Thomson RJ, Kelleher NL.

ACS Chem Biol. 2016 Dec 16;11(12):3452-3460. Epub 2016 Nov 15.


Classic Spotlight: What's on (in) Your Plate Today?

Metcalf WW.

J Bacteriol. 2016 Oct 7;198(21):2897-2898. Print 2016 Nov 1. No abstract available.


Quinovosamycins: new tunicamycin-type antibiotics in which the α, β-1″,11'-linked N-acetylglucosamine residue is replaced by N-acetylquinovosamine.

Price NP, Labeda DP, Naumann TA, Vermillion KE, Bowman MJ, Berhow MA, Metcalf WW, Bischoff KM.

J Antibiot (Tokyo). 2016 Aug;69(8):637-46. doi: 10.1038/ja.2016.49. Epub 2016 May 18.


Metabologenomics: Correlation of Microbial Gene Clusters with Metabolites Drives Discovery of a Nonribosomal Peptide with an Unusual Amino Acid Monomer.

Goering AW, McClure RA, Doroghazi JR, Albright JC, Haverland NA, Zhang Y, Ju KS, Thomson RJ, Metcalf WW, Kelleher NL.

ACS Cent Sci. 2016 Feb 24;2(2):99-108. doi: 10.1021/acscentsci.5b00331. Epub 2016 Jan 20.


Classic Spotlight: Electron Bifurcation, a Unifying Concept for Energy Conservation in Anaerobes.

Metcalf WW.

J Bacteriol. 2016 Apr 14;198(9):1358. doi: 10.1128/JB.00185-16. Print 2016 May. No abstract available.


Taxonomic evaluation of species in the Streptomyces hirsutus clade using multi-locus sequence analysis and proposals to reclassify several species in this clade.

Labeda DP, Rong X, Huang Y, Doroghazi JR, Ju KS, Metcalf WW.

Int J Syst Evol Microbiol. 2016 Jun;66(6):2444-50. doi: 10.1099/ijsem.0.001017. Epub 2016 Mar 11.


Metagenomic evidence for reciprocal particle exchange between the mainstem estuary and lateral bay sediments of the lower Columbia River.

Smith MW, Davis RE, Youngblut ND, Kärnä T, Herfort L, Whitaker RJ, Metcalf WW, Tebo BM, Baptista AM, Simon HM.

Front Microbiol. 2015 Oct 1;6:1074. doi: 10.3389/fmicb.2015.01074. eCollection 2015.


Genetic, Genomic, and Transcriptomic Studies of Pyruvate Metabolism in Methanosarcina barkeri Fusaro.

López Muñoz MM, Schönheit P, Metcalf WW.

J Bacteriol. 2015 Nov;197(22):3592-600. doi: 10.1128/JB.00551-15. Epub 2015 Sep 8.


Conserved biosynthetic pathways for phosalacine, bialaphos and newly discovered phosphonic acid natural products.

Blodgett JA, Zhang JK, Yu X, Metcalf WW.

J Antibiot (Tokyo). 2016 Jan;69(1):15-25. doi: 10.1038/ja.2015.77. Epub 2015 Sep 2.


Discovery of phosphonic acid natural products by mining the genomes of 10,000 actinomycetes.

Ju KS, Gao J, Doroghazi JR, Wang KK, Thibodeaux CJ, Li S, Metzger E, Fudala J, Su J, Zhang JK, Lee J, Cioni JP, Evans BS, Hirota R, Labeda DP, van der Donk WA, Metcalf WW.

Proc Natl Acad Sci U S A. 2015 Sep 29;112(39):12175-80. doi: 10.1073/pnas.1500873112. Epub 2015 Aug 31.


Genomic and phenotypic differentiation among Methanosarcina mazei populations from Columbia River sediment.

Youngblut ND, Wirth JS, Henriksen JR, Smith M, Simon H, Metcalf WW, Whitaker RJ.

ISME J. 2015 Oct;9(10):2191-205. doi: 10.1038/ismej.2015.31. Epub 2015 Mar 10.


Genetic basis for metabolism of methylated sulfur compounds in Methanosarcina species.

Fu H, Metcalf WW.

J Bacteriol. 2015 Apr;197(8):1515-24. doi: 10.1128/JB.02605-14. Epub 2015 Feb 17.


A roadmap for natural product discovery based on large-scale genomics and metabolomics.

Doroghazi JR, Albright JC, Goering AW, Ju KS, Haines RR, Tchalukov KA, Labeda DP, Kelleher NL, Metcalf WW.

Nat Chem Biol. 2014 Nov;10(11):963-8. doi: 10.1038/nchembio.1659. Epub 2014 Sep 28.


A multienzyme complex channels substrates and electrons through acetyl-CoA and methane biosynthesis pathways in Methanosarcina.

Lieber DJ, Catlett J, Madayiputhiya N, Nandakumar R, Lopez MM, Metcalf WW, Buan NR.

PLoS One. 2014 Sep 18;9(9):e107563. doi: 10.1371/journal.pone.0107563. eCollection 2014.


Towards a computational model of a methane producing archaeum.

Peterson JR, Labhsetwar P, Ellermeier JR, Kohler PR, Jain A, Ha T, Metcalf WW, Luthey-Schulten Z.

Archaea. 2014 Mar 4;2014:898453. doi: 10.1155/2014/898453. eCollection 2014.


Purification and characterization of phosphonoglycans from Glycomyces sp. strain NRRL B-16210 and Stackebrandtia nassauensis NRRL B-16338.

Yu X, Price NP, Evans BS, Metcalf WW.

J Bacteriol. 2014 May;196(9):1768-79. doi: 10.1128/JB.00036-14. Epub 2014 Feb 28.


Cyanohydrin phosphonate natural product from Streptomyces regensis.

Cioni JP, Doroghazi JR, Ju KS, Yu X, Evans BS, Lee J, Metcalf WW.

J Nat Prod. 2014 Feb 28;77(2):243-9. doi: 10.1021/np400722m. Epub 2014 Jan 17.


ITEP: an integrated toolkit for exploration of microbial pan-genomes.

Benedict MN, Henriksen JR, Metcalf WW, Whitaker RJ, Price ND.

BMC Genomics. 2014 Jan 3;15:8. doi: 10.1186/1471-2164-15-8.


Use of a phosphonate methyltransferase in the identification of the fosfazinomycin biosynthetic gene cluster.

Gao J, Ju KS, Yu X, Velásquez JE, Mukherjee S, Lee J, Zhao C, Evans BS, Doroghazi JR, Metcalf WW, van der Donk WA.

Angew Chem Int Ed Engl. 2014 Jan 27;53(5):1334-7. doi: 10.1002/anie.201308363. Epub 2013 Dec 27.


Diversity and abundance of phosphonate biosynthetic genes in nature.

Yu X, Doroghazi JR, Janga SC, Zhang JK, Circello B, Griffin BM, Labeda DP, Metcalf WW.

Proc Natl Acad Sci U S A. 2013 Dec 17;110(51):20759-64. doi: 10.1073/pnas.1315107110. Epub 2013 Dec 2.


Taxonomic evaluation of Streptomyces albus and related species using multilocus sequence analysis and proposals to emend the description of Streptomyces albus and describe Streptomyces pathocidini sp. nov.

Labeda DP, Doroghazi JR, Ju KS, Metcalf WW.

Int J Syst Evol Microbiol. 2014 Mar;64(Pt 3):894-900. doi: 10.1099/ijs.0.058107-0. Epub 2013 Nov 25.


Genomics-enabled discovery of phosphonate natural products and their biosynthetic pathways.

Ju KS, Doroghazi JR, Metcalf WW.

J Ind Microbiol Biotechnol. 2014 Feb;41(2):345-56. doi: 10.1007/s10295-013-1375-2. Epub 2013 Nov 24. Review.


Strain-specific proteogenomics accelerates the discovery of natural products via their biosynthetic pathways.

Albright JC, Goering AW, Doroghazi JR, Metcalf WW, Kelleher NL.

J Ind Microbiol Biotechnol. 2014 Feb;41(2):451-9. doi: 10.1007/s10295-013-1373-4. Epub 2013 Nov 19.


Comparative genomics of actinomycetes with a focus on natural product biosynthetic genes.

Doroghazi JR, Metcalf WW.

BMC Genomics. 2013 Sep 11;14:611. doi: 10.1186/1471-2164-14-611.


Discovery of the antibiotic phosacetamycin via a new mass spectrometry-based method for phosphonic acid detection.

Evans BS, Zhao C, Gao J, Evans CM, Ju KS, Doroghazi JR, van der Donk WA, Kelleher NL, Metcalf WW.

ACS Chem Biol. 2013 May 17;8(5):908-13. doi: 10.1021/cb400102t. Epub 2013 Mar 13.


Genomically and biochemically accurate metabolic reconstruction of Methanosarcina barkeri Fusaro, iMG746.

Gonnerman MC, Benedict MN, Feist AM, Metcalf WW, Price ND.

Biotechnol J. 2013 Sep;8(9):1070-9. doi: 10.1002/biot.201200266. Epub 2013 Mar 26.


Synthesis of methylphosphonic acid by marine microbes: a source for methane in the aerobic ocean.

Metcalf WW, Griffin BM, Cicchillo RM, Gao J, Janga SC, Cooke HA, Circello BT, Evans BS, Martens-Habbena W, Stahl DA, van der Donk WA.

Science. 2012 Aug 31;337(6098):1104-7. doi: 10.1126/science.1219875.


Genetic manipulation of Methanosarcina spp.

Kohler PR, Metcalf WW.

Front Microbiol. 2012 Jul 24;3:259. doi: 10.3389/fmicb.2012.00259. eCollection 2012.


Different biosynthetic pathways to fosfomycin in Pseudomonas syringae and Streptomyces species.

Kim SY, Ju KS, Metcalf WW, Evans BS, Kuzuyama T, van der Donk WA.

Antimicrob Agents Chemother. 2012 Aug;56(8):4175-83. doi: 10.1128/AAC.06478-11. Epub 2012 May 21.

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