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Items: 1 to 50 of 172

1.

Structure and function of an unusual flavodoxin from the domain Archaea.

Prakash D, Iyer PR, Suharti S, Walters KA, Santiago-Martinez MG, Golbeck JH, Murakami KS, Ferry JG.

Proc Natl Acad Sci U S A. 2019 Dec 4. pii: 201908578. doi: 10.1073/pnas.1908578116. [Epub ahead of print]

PMID:
31801875
2.

Life on the thermodynamic edge: Respiratory growth of an acetotrophic methanogen.

Prakash D, Chauhan SS, Ferry JG.

Sci Adv. 2019 Aug 21;5(8):eaaw9059. doi: 10.1126/sciadv.aaw9059. eCollection 2019 Aug.

3.

Comparative Genomics of the Genus Methanohalophilus, Including a Newly Isolated Strain From Kebrit Deep in the Red Sea.

Guan Y, Ngugi DK, Vinu M, Blom J, Alam I, Guillot S, Ferry JG, Stingl U.

Front Microbiol. 2019 Apr 24;10:839. doi: 10.3389/fmicb.2019.00839. eCollection 2019.

4.

Electron and Proton Flux for Carbon Dioxide Reduction in Methanosarcina barkeri During Direct Interspecies Electron Transfer.

Holmes DE, Rotaru AE, Ueki T, Shrestha PM, Ferry JG, Lovley DR.

Front Microbiol. 2018 Dec 13;9:3109. doi: 10.3389/fmicb.2018.03109. eCollection 2018.

5.

Methane on Mars and Habitability: Challenges and Responses.

Yung YL, Chen P, Nealson K, Atreya S, Beckett P, Blank JG, Ehlmann B, Eiler J, Etiope G, Ferry JG, Forget F, Gao P, Hu R, Kleinböhl A, Klusman R, Lefèvre F, Miller C, Mischna M, Mumma M, Newman S, Oehler D, Okumura M, Oremland R, Orphan V, Popa R, Russell M, Shen L, Sherwood Lollar B, Staehle R, Stamenković V, Stolper D, Templeton A, Vandaele AC, Viscardy S, Webster CR, Wennberg PO, Wong ML, Worden J.

Astrobiology. 2018 Oct;18(10):1221-1242. doi: 10.1089/ast.2018.1917. Epub 2018 Sep 19. Review.

6.

Electron Bifurcation and Confurcation in Methanogenesis and Reverse Methanogenesis.

Yan Z, Ferry JG.

Front Microbiol. 2018 Jun 20;9:1322. doi: 10.3389/fmicb.2018.01322. eCollection 2018. Review.

7.

Toward a mechanistic and physiological understanding of a ferredoxin:disulfide reductase from the domains Archaea and Bacteria.

Prakash D, Walters KA, Martinie RJ, McCarver AC, Kumar AK, Lessner DJ, Krebs C, Golbeck JH, Ferry JG.

J Biol Chem. 2018 Jun 15;293(24):9198-9209. doi: 10.1074/jbc.RA118.002473. Epub 2018 May 2.

8.

A biochemical framework for anaerobic oxidation of methane driven by Fe(III)-dependent respiration.

Yan Z, Joshi P, Gorski CA, Ferry JG.

Nat Commun. 2018 Apr 24;9(1):1642. doi: 10.1038/s41467-018-04097-9.

9.

Sulphonamide inhibition studies of the β-carbonic anhydrase from the bacterial pathogen Clostridium perfringens.

Vullo D, Kumar RSS, Scozzafava A, Ferry JG, Supuran CT.

J Enzyme Inhib Med Chem. 2018 Dec;33(1):31-36. doi: 10.1080/14756366.2017.1388233.

10.

Single-cell genomics reveals pyrrolysine-encoding potential in members of uncultivated archaeal candidate division MSBL1.

Guan Y, Haroon MF, Alam I, Ferry JG, Stingl U.

Environ Microbiol Rep. 2017 Aug;9(4):404-410. doi: 10.1111/1758-2229.12545. Epub 2017 Jun 6.

PMID:
28493460
11.
12.

Functional Role of MrpA in the MrpABCDEFG Na+/H+ Antiporter Complex from the Archaeon Methanosarcina acetivorans.

Jasso-Chávez R, Diaz-Perez C, Rodríguez-Zavala JS, Ferry JG.

J Bacteriol. 2016 Dec 28;199(2). pii: e00662-16. doi: 10.1128/JB.00662-16. Print 2017 Jan 15.

13.

Assessing methanotrophy and carbon fixation for biofuel production by Methanosarcina acetivorans.

Nazem-Bokaee H, Gopalakrishnan S, Ferry JG, Wood TK, Maranas CD.

Microb Cell Fact. 2016 Jan 17;15:10. doi: 10.1186/s12934-015-0404-4.

14.

Reversing methanogenesis to capture methane for liquid biofuel precursors.

Soo VW, McAnulty MJ, Tripathi A, Zhu F, Zhang L, Hatzakis E, Smith PB, Agrawal S, Nazem-Bokaee H, Gopalakrishnan S, Salis HM, Ferry JG, Maranas CD, Patterson AD, Wood TK.

Microb Cell Fact. 2016 Jan 14;15:11. doi: 10.1186/s12934-015-0397-z.

15.

Structural and Biochemical Characterizations of Methanoredoxin from Methanosarcina acetivorans, a Glutaredoxin-Like Enzyme with Coenzyme M-Dependent Protein Disulfide Reductase Activity.

Yenugudhati D, Prakash D, Kumar AK, Kumar RS, Yennawar NH, Yennawar HP, Ferry JG.

Biochemistry. 2016 Jan 19;55(2):313-21. doi: 10.1021/acs.biochem.5b00823. Epub 2015 Dec 30.

PMID:
26684934
16.

A Ferredoxin Disulfide Reductase Delivers Electrons to the Methanosarcina barkeri Class III Ribonucleotide Reductase.

Wei Y, Li B, Prakash D, Ferry JG, Elliott SJ, Stubbe J.

Biochemistry. 2015 Dec 1;54(47):7019-28. doi: 10.1021/acs.biochem.5b01092. Epub 2015 Nov 19.

17.

Essential Amino Acid Supplementation by Gut Microbes of a Wood-Feeding Cerambycid.

Ayayee PA, Larsen T, Rosa C, Felton GW, Ferry JG, Hoover K.

Environ Entomol. 2016 Feb;45(1):66-73. doi: 10.1093/ee/nvv153. Epub 2015 Sep 22.

18.

Acetate Metabolism in Anaerobes from the Domain Archaea.

Ferry JG.

Life (Basel). 2015 Jun 9;5(2):1454-71. doi: 10.3390/life5021454. Review.

19.

Structural and Biochemical Characterization of a Ferredoxin:Thioredoxin Reductase-like Enzyme from Methanosarcina acetivorans.

Kumar AK, Kumar RS, Yennawar NH, Yennawar HP, Ferry JG.

Biochemistry. 2015 May 19;54(19):3122-8.

PMID:
25915695
20.

Methane oxidation by anaerobic archaea for conversion to liquid fuels.

Mueller TJ, Grisewood MJ, Nazem-Bokaee H, Gopalakrishnan S, Ferry JG, Wood TK, Maranas CD.

J Ind Microbiol Biotechnol. 2015 Mar;42(3):391-401. doi: 10.1007/s10295-014-1548-7. Epub 2014 Nov 27. Review.

PMID:
25427790
21.

Draft Genome Sequence of an Obligately Methylotrophic Methanogen, Methanococcoides methylutens, Isolated from Marine Sediment.

Guan Y, Ngugi DK, Blom J, Ali S, Ferry JG, Stingl U.

Genome Announc. 2014 Nov 20;2(6). pii: e01184-14. doi: 10.1128/genomeA.01184-14.

22.

Gut microbes contribute to nitrogen provisioning in a wood-feeding cerambycid.

Ayayee P, Rosa C, Ferry JG, Felton G, Saunders M, Hoover K.

Environ Entomol. 2014 Aug;43(4):903-12. doi: 10.1603/EN14045. Epub 2014 Jun 16.

PMID:
24937261
23.

Characterization of the RnfB and RnfG subunits of the Rnf complex from the archaeon Methanosarcina acetivorans.

Suharti S, Wang M, de Vries S, Ferry JG.

PLoS One. 2014 May 16;9(5):e97966. doi: 10.1371/journal.pone.0097966. eCollection 2014.

24.

Anion inhibition studies of a β-carbonic anhydrase from Clostridium perfringens.

Vullo D, Sai Kumar RS, Scozzafava A, Capasso C, Ferry JG, Supuran CT.

Bioorg Med Chem Lett. 2013 Dec 15;23(24):6706-10. doi: 10.1016/j.bmcl.2013.10.037. Epub 2013 Oct 29.

PMID:
24210500
25.

Prokaryotic carbonic anhydrases of Earth's environment.

Kumar RS, Ferry JG.

Subcell Biochem. 2014;75:77-87. doi: 10.1007/978-94-007-7359-2_5. Review.

PMID:
24146375
26.

MrpA functions in energy conversion during acetate-dependent growth of Methanosarcina acetivorans.

Jasso-Chávez R, Apolinario EE, Sowers KR, Ferry JG.

J Bacteriol. 2013 Sep;195(17):3987-94. doi: 10.1128/JB.00581-13. Epub 2013 Jul 8. Erratum in: J Bacteriol. 2014 Feb;196(3):716.

27.

Frontiers, opportunities, and challenges in biochemical and chemical catalysis of CO2 fixation.

Appel AM, Bercaw JE, Bocarsly AB, Dobbek H, DuBois DL, Dupuis M, Ferry JG, Fujita E, Hille R, Kenis PJ, Kerfeld CA, Morris RH, Peden CH, Portis AR, Ragsdale SW, Rauchfuss TB, Reek JN, Seefeldt LC, Thauer RK, Waldrop GL.

Chem Rev. 2013 Aug 14;113(8):6621-58. doi: 10.1021/cr300463y. Epub 2013 Jun 14. Review. No abstract available.

28.

Biochemistry and physiology of the β class carbonic anhydrase (Cpb) from Clostridium perfringens strain 13.

Kumar RS, Hendrick W, Correll JB, Patterson AD, Melville SB, Ferry JG.

J Bacteriol. 2013 May;195(10):2262-9. doi: 10.1128/JB.02288-12. Epub 2013 Mar 8.

29.

Carbonic anhydrases of anaerobic microbes.

Ferry JG.

Bioorg Med Chem. 2013 Mar 15;21(6):1392-5. doi: 10.1016/j.bmc.2012.12.005. Epub 2012 Dec 13.

PMID:
23267670
30.

Role of Trp19 and Tyr200 in catalysis by the γ-class carbonic anhydrase from Methanosarcina thermophila.

Zimmerman S, Domsic JF, Tu C, Robbins AH, McKenna R, Silverman DN, Ferry JG.

Arch Biochem Biophys. 2013 Jan 1;529(1):11-7. doi: 10.1016/j.abb.2012.10.010. Epub 2012 Oct 27.

31.

MreA functions in the global regulation of methanogenic pathways in Methanosarcina acetivorans.

Reichlen MJ, Vepachedu VR, Murakami KS, Ferry JG.

MBio. 2012 Jul 31;3(4):e00189-12. doi: 10.1128/mBio.00189-12. Print 2012.

32.

Role of the fused corrinoid/methyl transfer protein CmtA during CO-dependent growth of Methanosarcina acetivorans.

Vepachedu VR, Ferry JG.

J Bacteriol. 2012 Aug;194(16):4161-8. doi: 10.1128/JB.00593-12. Epub 2012 May 25. Erratum in: J Bacteriol. 2012 Nov;194(21):6016.

33.

Expression, purification, crystallization and preliminary X-ray crystallographic analysis of a novel plant-type ferredoxin/thioredoxin reductase-like protein from Methanosarcina acetivorans.

Kumar AK, Yennawar NH, Yennawar HP, Ferry JG.

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2011 Jul 1;67(Pt 7):775-8. doi: 10.1107/S1744309111017234. Epub 2011 Jun 30.

34.

Electron transport in acetate-grown Methanosarcina acetivorans.

Wang M, Tomb JF, Ferry JG.

BMC Microbiol. 2011 Jul 24;11:165. doi: 10.1186/1471-2180-11-165.

35.

Fundamentals of methanogenic pathways that are key to the biomethanation of complex biomass.

Ferry JG.

Curr Opin Biotechnol. 2011 Jun;22(3):351-7. doi: 10.1016/j.copbio.2011.04.011. Epub 2011 May 17. Review.

36.

Acetate kinase and phosphotransacetylase.

Ferry JG.

Methods Enzymol. 2011;494:219-31. doi: 10.1016/B978-0-12-385112-3.00011-1.

PMID:
21402217
37.

Metabolic reconstruction of the archaeon methanogen Methanosarcina Acetivorans.

Satish Kumar V, Ferry JG, Maranas CD.

BMC Syst Biol. 2011 Feb 15;5:28. doi: 10.1186/1752-0509-5-28.

38.

An engineered methanogenic pathway derived from the domains Bacteria and Archaea.

Lessner DJ, Lhu L, Wahal CS, Ferry JG.

MBio. 2010 Nov 2;1(5). pii: e00243-10. doi: 10.1128/mBio.00243-10.

39.

How to make a living by exhaling methane.

Ferry JG.

Annu Rev Microbiol. 2010;64:453-73. doi: 10.1146/annurev.micro.112408.134051. Review.

PMID:
20528692
40.

Functional analysis of the three TATA binding protein homologs in Methanosarcina acetivorans.

Reichlen MJ, Murakami KS, Ferry JG.

J Bacteriol. 2010 Mar;192(6):1511-7. doi: 10.1128/JB.01165-09. Epub 2010 Jan 15.

41.

Characterization of CamH from Methanosarcina thermophila, founding member of a subclass of the {gamma} class of carbonic anhydrases.

Zimmerman SA, Tomb JF, Ferry JG.

J Bacteriol. 2010 Mar;192(5):1353-60. doi: 10.1128/JB.01164-09. Epub 2009 Dec 18.

42.

The gamma class of carbonic anhydrases.

Ferry JG.

Biochim Biophys Acta. 2010 Feb;1804(2):374-81. doi: 10.1016/j.bbapap.2009.08.026. Epub 2009 Sep 10. Review.

43.
44.

Methanolobus zinderi sp. nov., a methylotrophic methanogen isolated from a deep subsurface coal seam.

Doerfert SN, Reichlen M, Iyer P, Wang M, Ferry JG.

Int J Syst Evol Microbiol. 2009 May;59(Pt 5):1064-9. doi: 10.1099/ijs.0.003772-0.

PMID:
19406794
45.

The archetype gamma-class carbonic anhydrase (Cam) contains iron when synthesized in vivo.

Macauley SR, Zimmerman SA, Apolinario EE, Evilia C, Hou YM, Ferry JG, Sowers KR.

Biochemistry. 2009 Feb 10;48(5):817-9. doi: 10.1021/bi802246s.

PMID:
19187031
46.

Carbonic anhydrase activators: activation of the archaeal beta-class (Cab) and gamma-class (Cam) carbonic anhydrases with amino acids and amines.

Innocenti A, Zimmerman SA, Scozzafava A, Ferry JG, Supuran CT.

Bioorg Med Chem Lett. 2008 Dec 1;18(23):6194-8. doi: 10.1016/j.bmcl.2008.10.005. Epub 2008 Oct 5.

PMID:
18930395
47.

Structural and biochemical characterization of flavoredoxin from the archaeon Methanosarcina acetivorans.

Suharti S, Murakami KS, de Vries S, Ferry JG.

Biochemistry. 2008 Nov 4;47(44):11528-35. doi: 10.1021/bi801012p. Epub 2008 Oct 9.

PMID:
18842001
48.

Methanogenesis in marine sediments.

Ferry JG, Lessner DJ.

Ann N Y Acad Sci. 2008 Mar;1125:147-57. doi: 10.1196/annals.1419.007.

PMID:
18378593
49.

The beta and gamma classes of carbonic anhydrase.

Zimmerman SA, Ferry JG.

Curr Pharm Des. 2008;14(7):716-21. Review.

PMID:
18336318
50.

Investigation of the Methanosarcina thermophila acetate kinase mechanism by fluorescence quenching.

Gorrell A, Ferry JG.

Biochemistry. 2007 Dec 11;46(49):14170-6. Epub 2007 Nov 14.

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