Experts and Doctors on methanosarcina in United States

Summary

Locale: United States
Topic: methanosarcina

Top Publications

  1. Price Whelan A, Dietrich L, Newman D. Rethinking 'secondary' metabolism: physiological roles for phenazine antibiotics. Nat Chem Biol. 2006;2:71-8 pubmed
    ..In this article, we suggest that phenazines, which are produced under conditions of high cell density and nutrient limitation, may be important for the persistence of pseudomonads in the environment. ..
  2. Li Q, Li L, Rejtar T, Karger B, Ferry J. Proteome of Methanosarcina acetivorans Part II: comparison of protein levels in acetate- and methanol-grown cells. J Proteome Res. 2005;4:129-35 pubmed
    ..The potential physiological basis for these novel patterns of protein synthesis are discussed. ..
  3. Horne A, Lessner D. Assessment of the oxidant tolerance of Methanosarcina acetivorans. FEMS Microbiol Lett. 2013;343:13-9 pubmed publisher
    ..acetivorans. Combined with recent advances in the genetic manipulation of methanogens, methods in assessment of methanogen oxidant tolerance will aid in the identification of components of the antioxidant defense systems. ..
  4. James C, Ferguson T, Leykam J, Krzycki J. The amber codon in the gene encoding the monomethylamine methyltransferase isolated from Methanosarcina barkeri is translated as a sense codon. J Biol Chem. 2001;276:34252-8 pubmed
    ..The amber codon is thus read through during translation at apparently high efficiency and corresponds to lysine in tryptic fragments of MtmB even though canonical lysine codon usage is encountered in other Methanosarcina genes. ..
  5. Mahapatra A, Patel A, Soares J, Larue R, Zhang J, Metcalf W, et al. Characterization of a Methanosarcina acetivorans mutant unable to translate UAG as pyrrolysine. Mol Microbiol. 2006;59:56-66 pubmed
    ..These results indicate that in-depth genetic analysis of UAG translation as pyrrolysine is feasible, as deletion of pylT is conditionally lethal depending on growth substrate. ..
  6. Suharti S, Murakami K, de Vries S, Ferry J. Structural and biochemical characterization of flavoredoxin from the archaeon Methanosarcina acetivorans. Biochemistry. 2008;47:11528-35 pubmed publisher
    ..The FMN is bound with hydrogen bonds to the isoalloxazine ring and electrostatic interactions with the phosphate moiety that, together with sequence analyses of homologues, indicate a novel FMN binding motif for the flavoredoxin family. ..
  7. Rao B, Maris E, Jackman J. tRNA 5'-end repair activities of tRNAHis guanylyltransferase (Thg1)-like proteins from Bacteria and Archaea. Nucleic Acids Res. 2011;39:1833-42 pubmed publisher
    ..These data support more widespread roles for 3'-5' nucleotide addition reactions in biology than previously expected. ..
  8. Longstaff D, Blight S, Zhang L, Green Church K, Krzycki J. In vivo contextual requirements for UAG translation as pyrrolysine. Mol Microbiol. 2007;63:229-41 pubmed
  9. Kisker C, Schindelin H, Alber B, Ferry J, Rees D. A left-hand beta-helix revealed by the crystal structure of a carbonic anhydrase from the archaeon Methanosarcina thermophila. EMBO J. 1996;15:2323-30 pubmed
    ..Based on sequence similarities, the structure of this enzyme is the prototype of a new class of carbonic anhydrases with representatives in all three phylogenetic domains of life. ..

More Information

Publications28

  1. Miles R, Gorrell A, Ferry J. Evidence for a transition state analog, MgADP-aluminum fluoride-acetate, in acetate kinase from Methanosarcina thermophila. J Biol Chem. 2002;277:22547-52 pubmed
    ..The protection from inhibition by a non-hydrolyzable ATP analog or acetylphosphate, in conjunction with the strict dependence of inhibition on the presence of both ADP and acetate, supports a direct in-line mechanism for acetate kinase. ..
  2. Gorrell A, Lawrence S, Ferry J. Structural and kinetic analyses of arginine residues in the active site of the acetate kinase from Methanosarcina thermophila. J Biol Chem. 2005;280:10731-42 pubmed
    ..Kinetic analyses of Arg(241) and Arg(91) replacement variants indicated that these residues are essential for catalysis and also indicated a role in binding acetate. ..
  3. Ferry J. Fundamentals of methanogenic pathways that are key to the biomethanation of complex biomass. Curr Opin Biotechnol. 2011;22:351-7 pubmed publisher
    ..This review covers recent advances in the fundamental understanding of both methanogenic pathways with the view of stimulating research towards improving the rate and reliability of the overall biomethanation process. ..
  4. Miles R, Iyer P, Ferry J. Site-directed mutational analysis of active site residues in the acetate kinase from Methanosarcina thermophila. J Biol Chem. 2001;276:45059-64 pubmed
    ..The results are discussed with respect to the acetate kinase catalytic mechanism and the relationship to other sugar kinase/Hsc70/actin superfamily members. ..
  5. Ferry J. Acetate kinase and phosphotransacetylase. Methods Enzymol. 2011;494:219-31 pubmed publisher
    ..The high identity of both enzymes to paralogs in the domain Bacteria suggests ancient origins and common mechanisms. ..
  6. Vepachedu V, Ferry J. Role of the fused corrinoid/methyl transfer protein CmtA during CO-dependent growth of Methanosarcina acetivorans. J Bacteriol. 2012;194:4161-8 pubmed publisher
    ..acetivorans. Thus, we propose that the name of the enzyme encoded by MA4384 be CmtA (for cytoplasmic methyltransferase). ..
  7. Bryson D, Fan C, Guo L, Miller C, Söll D, Liu D. Continuous directed evolution of aminoacyl-tRNA synthetases. Nat Chem Biol. 2017;13:1253-1260 pubmed publisher
    ..These findings offer new AARSs that increase the utility of orthogonal translation systems and establish the capability of PACE to efficiently evolve orthogonal AARSs with high activity and amino acid specificity. ..
  8. Burke S, Krzycki J. Reconstitution of Monomethylamine:Coenzyme M methyl transfer with a corrinoid protein and two methyltransferases purified from Methanosarcina barkeri. J Biol Chem. 1997;272:16570-7 pubmed
    ..MMAMT functions as a MMA:MMCP methyltransferase, while MT2-A functions as a methyl-MMCP:CoM methyltransferase...
  9. Zayas C, Woodson J, Escalante Semerena J. The cobZ gene of Methanosarcina mazei Go1 encodes the nonorthologous replacement of the alpha-ribazole-5'-phosphate phosphatase (CobC) enzyme of Salmonella enterica. J Bacteriol. 2006;188:2740-3 pubmed
    ..strain NRC-1. A strain of the latter carrying an in-frame deletion of ORF Vng1577 was not a cobalamin auxotroph, suggesting that either there is redundancy of this function in Halobacterium or the gene was misannotated...
  10. Woodson J, Escalante Semerena J. CbiZ, an amidohydrolase enzyme required for salvaging the coenzyme B12 precursor cobinamide in archaea. Proc Natl Acad Sci U S A. 2004;101:3591-6 pubmed publisher
    ..Reasons for the evolution of two distinct pathways for Cbi salvaging in prokaryotes are discussed...
  11. Paul L, Ferguson D, Krzycki J. The trimethylamine methyltransferase gene and multiple dimethylamine methyltransferase genes of Methanosarcina barkeri contain in-frame and read-through amber codons. J Bacteriol. 2000;182:2520-9 pubmed
    ..Thus, the genes encoding the three types of methyltransferases that initiate methanogenesis from methylamine contain in-frame amber codons that are suppressed during expression of the characterized methyltransferases...
  12. Lee M, Jiang R, Jain R, Larue R, Krzycki J, Chan M. Structure of Desulfitobacterium hafniense PylSc, a pyrrolysyl-tRNA synthetase. Biochem Biophys Res Commun. 2008;374:470-4 pubmed publisher
    ..In PylSc, the hydrophobic pocket binding the ring of pyrrolysine is more constrained than in the archaeal enzyme; other structural differences are also apparent...
  13. Graham D, Taylor S, Wolf R, Namboori S. Convergent evolution of coenzyme M biosynthesis in the Methanosarcinales: cysteate synthase evolved from an ancestral threonine synthase. Biochem J. 2009;424:467-78 pubmed publisher
    ..These differences in coenzyme M biosynthesis afford the opportunity to develop methanogen inhibitors that discriminate between the classes of methanogenic archaea...
  14. Gorrell A, Ferry J. Investigation of the Methanosarcina thermophila acetate kinase mechanism by fluorescence quenching. Biochemistry. 2007;46:14170-6 pubmed
  15. Longstaff D, Larue R, Faust J, Mahapatra A, Zhang L, Green Church K, et al. A natural genetic code expansion cassette enables transmissible biosynthesis and genetic encoding of pyrrolysine. Proc Natl Acad Sci U S A. 2007;104:1021-6 pubmed
    ..Analogous cassettes may have served similar functions for other amino acids during the evolutionary expansion of the canonical genetic code. ..
  16. Gaston M, Zhang L, Green Church K, Krzycki J. The complete biosynthesis of the genetically encoded amino acid pyrrolysine from lysine. Nature. 2011;471:647-50 pubmed publisher
    ..Furthermore, intermediates of the pathway may provide new avenues by which the pyl system can be exploited to produce recombinant proteins with useful modified residues...
  17. Wang M, Tomb J, Ferry J. Electron transport in acetate-grown Methanosarcina acetivorans. BMC Microbiol. 2011;11:165 pubmed publisher
    ..Thus, the membrane-bound electron transport chain of acetate-grown M. acetivorans was investigated to advance a more complete understanding of acetotrophic methanogens...
  18. Leartsakulpanich U, Antonkine M, Ferry J. Site-specific mutational analysis of a novel cysteine motif proposed to ligate the 4Fe-4S cluster in the iron-sulfur flavoprotein of the thermophilic methanoarchaeon Methanosarcina thermophila. J Bacteriol. 2000;182:5309-16 pubmed
    ..The combined results of this study support a role for the novel CX(2)CX(2)CX(4-7)C motif in ligating the 4Fe-4S clusters in Isf and Isf homologues. ..
  19. Jasso Ch vez R, Apolinario E, Sowers K, Ferry J. MrpA functions in energy conversion during acetate-dependent growth of Methanosarcina acetivorans. J Bacteriol. 2013;195:3987-94 pubmed publisher
    ..The results indicated that the Mrp complex is essential for efficient ATP synthesis and optimal growth at the low concentrations of acetate encountered in the environment...