Giles, Teresa N, Fisher, Derek J, Graham, David E
Abstract Background Chlamydia have reduced genomes that reflect their obligately parasitic lifestyle. Despite their different tissue tropisms, chlamydial strains share a large number of common genes...
McCloskey, James A., Graham, David E., Zhou, Shaolian, Crain, Pamela F., Ibba, Michael, Konisky, Jordan, ...
Post-transcriptional modifications in archaeal RNA are known to be phylogenetically distinct but relatively little is known of tRNA from the Methanococci, a lineage of methanogenic marine euryarchaea...
The United States is currently undergoing two periods of simultaneous transition the first involving significant changes in the international environment, the second centered around a transformation...
Graham, David E., Overbeek, Ross, Olsen, Gary J., Woese, Carl R.
Comparisons of complete genome sequences allow the most objective and comprehensive descriptions possible of a lineage's evolution. This communication uses the completed genomes from four major...
McCloskey, James A., Graham, David E., Zhou, Shaolian, Crain, Pamela F., Ibba, Michael, Konisky, Jordan, ...
Post-transcriptional modifications in archaeal RNA are known to be phylogenetically distinct but relatively little is known of tRNA from the Methanococci, a lineage of methanogenic marine euryarchaea...
Kim, Alexander D., Graham, David E., Seeholzer, Steven H., Markham, George D.
Polyamines are present in high concentrations in archaea, yet little is known about their synthesis, except by extrapolation from bacterial and eucaryal systems. S-Adenosylmethionine (AdoMet)...
Transfer RNA-dependent amino acid biosynthesis: An essential route to asparagine formation
Min, Bokkee, Pelaschier, Joanne T., Graham, David E., Tumbula-Hansen, Debra, Söll, Dieter
Biochemical experiments and genomic sequence analysis showed that Deinococcus radiodurans and Thermus thermophilus do not possess asparagine synthetase (encoded by asnA or asnB), the enzyme forming...
Orthologs of a novel archaeal and of the bacterial peptidyl–tRNA hydrolase are nonessential in yeast
Rosas-Sandoval, Guillermina, Ambrogelly, Alexandre, Rinehart, Jesse, Wei, David, Cruz-Vera, L. Rogelio, Graham, David E., ...
Peptidyl–tRNA hydrolase (encoded by pth) is an essential enzyme in all bacteria, where it releases tRNA from the premature translation termination product peptidyl–tRNA. Archaeal genomes lack a...
Phosphoprotein with Phosphoglycerate Mutase Activity from the Archaeon Sulfolobus solfataricus
Potters, M. Ben, Solow, Barbara T., Bischoff, Kenneth M., Graham, David E., Lower, Brian H., Helm, Richard, ...
When soluble extracts of the extreme acidothermophilic archaeon Sulfolobus solfataricus were incubated with [γ-32P]ATP, several proteins were radiolabeled. One of the more prominent of these, which...
The Genome of M. acetivorans Reveals Extensive Metabolic and Physiological Diversity
Galagan, James E., Nusbaum, Chad, Roy, Alice, Endrizzi, Matthew G., Macdonald, Pendexter, FitzHugh, Will, ...
Methanogenesis, the biological production of methane, plays a pivotal role in the global carbon cycle and contributes significantly to global warming. The majority of methane in nature is derived...
Li, Hong, Xu, Huimin, Graham, David E., White, Robert H.
Proteins in the ATP-grasp superfamily of amide bond-forming ligases have evolved to function in a number of unrelated biosynthetic pathways. Previously identified homologs encoding glutathione...
The genome of Nanoarchaeum equitans: Insights into early archaeal evolution and derived parasitism
Waters, Elizabeth, Hohn, Michael J., Ahel, Ivan, Graham, David E., Adams, Mark D., Barnstead, Mary, ...
The hyperthermophile Nanoarchaeum equitans is an obligate symbiont growing in coculture with the crenarchaeon Ignicoccus. Ribosomal protein and rRNA-based phylogenies place its branching point early...
Graham, David E., Overbeek, Ross, Olsen, Gary J., Woese, Carl R.
Comparisons of complete genome sequences allow the most objective and comprehensive descriptions possible of a lineage's evolution. This communication uses the completed genomes from four major...
McCloskey, James A., Graham, David E., Zhou, Shaolian, Crain, Pamela F., Ibba, Michael, Konisky, Jordan, ...
Post-transcriptional modifications in archaeal RNA are known to be phylogenetically distinct but relatively little is known of tRNA from the Methanococci, a lineage of methanogenic marine euryarchaea...
Kim, Alexander D., Graham, David E., Seeholzer, Steven H., Markham, George D.
Polyamines are present in high concentrations in archaea, yet little is known about their synthesis, except by extrapolation from bacterial and eucaryal systems. S-Adenosylmethionine (AdoMet)...
Transfer RNA-dependent amino acid biosynthesis: An essential route to asparagine formation
Min, Bokkee, Pelaschier, Joanne T., Graham, David E., Tumbula-Hansen, Debra, Söll, Dieter
Biochemical experiments and genomic sequence analysis showed that Deinococcus radiodurans and Thermus thermophilus do not possess asparagine synthetase (encoded by asnA or asnB), the enzyme forming...
Orthologs of a novel archaeal and of the bacterial peptidyl–tRNA hydrolase are nonessential in yeast
Rosas-Sandoval, Guillermina, Ambrogelly, Alexandre, Rinehart, Jesse, Wei, David, Cruz-Vera, L. Rogelio, Graham, David E., ...
Peptidyl–tRNA hydrolase (encoded by pth) is an essential enzyme in all bacteria, where it releases tRNA from the premature translation termination product peptidyl–tRNA. Archaeal genomes lack a...
Phosphoprotein with Phosphoglycerate Mutase Activity from the Archaeon Sulfolobus solfataricus
Potters, M. Ben, Solow, Barbara T., Bischoff, Kenneth M., Graham, David E., Lower, Brian H., Helm, Richard, ...
When soluble extracts of the extreme acidothermophilic archaeon Sulfolobus solfataricus were incubated with [γ-32P]ATP, several proteins were radiolabeled. One of the more prominent of these, which...
The Genome of M. acetivorans Reveals Extensive Metabolic and Physiological Diversity
Galagan, James E., Nusbaum, Chad, Roy, Alice, Endrizzi, Matthew G., Macdonald, Pendexter, FitzHugh, Will, ...
Methanogenesis, the biological production of methane, plays a pivotal role in the global carbon cycle and contributes significantly to global warming. The majority of methane in nature is derived...
Li, Hong, Xu, Huimin, Graham, David E., White, Robert H.
Proteins in the ATP-grasp superfamily of amide bond-forming ligases have evolved to function in a number of unrelated biosynthetic pathways. Previously identified homologs encoding glutathione...
The genome of Nanoarchaeum equitans: Insights into early archaeal evolution and derived parasitism
Waters, Elizabeth, Hohn, Michael J., Ahel, Ivan, Graham, David E., Adams, Mark D., Barnstead, Mary, ...
The hyperthermophile Nanoarchaeum equitans is an obligate symbiont growing in coculture with the crenarchaeon Ignicoccus. Ribosomal protein and rRNA-based phylogenies place its branching point early...
Biosynthesis of Phosphoserine in the Methanococcales▿
Helgadóttir, Sunna, Rosas-Sandoval, Guillermina, Söll, Dieter, Graham, David E.
Methanococcus maripaludis and Methanocaldococcus jannaschii produce cysteine for protein synthesis using a tRNA-dependent pathway. These methanogens charge tRNACys with l-phosphoserine, which is also...
Enzymology and Evolution of the Pyruvate Pathway to 2-Oxobutyrate in Methanocaldococcus jannaschii▿
Drevland, Randy M., Waheed, Abdul, Graham, David E.
The archaeon Methanocaldococcus jannaschii uses three different 2-oxoacid elongation pathways, which extend the chain length of precursors in leucine, isoleucine, and coenzyme B biosyntheses. In each...
Characterization of an Acid-Dependent Arginine Decarboxylase Enzyme from Chlamydophila pneumoniae▿
Giles, Teresa N., Graham, David E.
Genome sequences from members of the Chlamydiales encode diverged homologs of a pyruvoyl-dependent arginine decarboxylase enzyme that nonpathogenic euryarchaea use in polyamine biosynthesis. The...
Acetamido Sugar Biosynthesis in the Euryarchaea▿ †
Namboori, Seema C., Graham, David E.
Archaea and eukaryotes share a dolichol phosphate-dependent system for protein N-glycosylation. In both domains, the acetamido sugar N-acetylglucosamine (GlcNAc) forms part of the core...
A korarchaeal genome reveals insights into the evolution of the Archaea
Elkins, James G., Podar, Mircea, Graham, David E., Makarova, Kira S., Wolf, Yuri, Randau, Lennart, ...
The candidate division Korarchaeota comprises a group of uncultivated microorganisms that, by their small subunit rRNA phylogeny, may have diverged early from the major archaeal phyla Crenarchaeota...
Smith, Conor B., Graham, David E.
Most chlamydial strains have a pyruvoyl-dependent decarboxylase protein that converts l-arginine to agmatine. However, chlamydiae do not produce arginine, so they must import it from their host....
Archaeal ApbC/Nbp35 Homologs Function as Iron-Sulfur Cluster Carrier Proteins▿ †
Boyd, Jeffrey M., Drevland, Randy M., Downs, Diana M., Graham, David E.
Iron-sulfur clusters may have been the earliest catalytic cofactors on earth, and most modern organisms use them extensively. Although members of the Archaea produce numerous iron-sulfur proteins,...
Crenarchaeal Arginine Decarboxylase Evolved from an S-Adenosylmethionine Decarboxylase Enzyme*S⃞
Giles, Teresa N., Graham, David E.
The crenarchaeon Sulfolobus solfataricus uses arginine to produce putrescine for polyamine biosynthesis. However, genome sequences from S. solfataricus and most crenarchaea have no known homologs of...
Methanogen Homoaconitase Catalyzes Both Hydrolyase Reactions in Coenzyme B Biosynthesis*S⃞
Drevland, Randy M., Jia, Yunhua, Palmer, David R. J., Graham, David E.
Homoaconitase enzymes catalyze hydrolyase reactions in the α-aminoadipate pathway for lysine biosynthesis or the 2-oxosuberate pathway for methanogenic coenzyme B biosynthesis. Despite the homology...