Erratum: The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus

Klenk, Hans Peter; Clayton, Rebecca A.; Tomb, Jean-François; White, Owen; Nelson, Karen E.; Ketchum, Karen A.; Dodaon, R. J.; Gwinn, Michelle L.; Hickey, Erin K.; Peterson, Jeremy; Richardson, D.; Kerlavage, Anthony R.; Graham, David E.; Kyrpides, Nikos C.; Fleischmann, Robert; Quackenbush, John; Lee, N. H.; Sutton, Granger; Gill, Sarjeet S.; Kirkness, Ewen F.; Dougherty, Brian; McKenney, Keith; Adams, Mark D.; Loftus, Brendan J.; Peterson, Stephanie; Reich, Claudia I.; McNeil, Leslie Klis; Badger, Jonathan H.; Glodek, Anna; Zhou, Lisha; Overbeek, Ross; Gocayne, Jeannine D.; Weldman, J. F.; McDonald, Lisa; Utterback, Teresa; Cotton, Matthew; Spriggs, Tracy; Artiach, Patricia; Kaine, Brian P.; Sykes, Sean M.; Sadow, P. W.; D’Andrea, Kurt; Bowman, Charles A.; Fujli, C.; Garland, Stacey; Mason, Tanya; Olsen, Gary J.; Fraser, Claire M.; Smith, Hamilton O.; Woese, C. R.; Venter, J. Craig

doi:10.1038/27963

Cited by 37 publications

(8 citation statements)

References 12 publications

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“…fulgidus is a hyperthermophylic sulfur-metabolizing organism. Its genome contains only two P-type ATPases encoding genes AF0473 and AF0152 (41). We will refer to these ATPases as CopA (NCB accession number AAB90763) (this has been previously referred as PacS) and CopB (NCB accession number AAB91079).…”

Section: Resultsmentioning

confidence: 99%

Characterization of a Thermophilic P-type Ag+/Cu+-ATPase from the ExtremophileArchaeoglobus fulgidus

Mandal

Cheung²,

Argüello

2002

Journal of Biological Chemistry

123

192

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The thermophilic, sulfur metabolizing Archaeoglobus fulgidus contains two genes, AF0473 and AF0152, encoding for PIB-type heavy metal transport ATPases. In this study, we describe the cloning, heterologous expression, purification, and functional characterization of one of these ATPases, CopA (NCB accession number AAB90763), encoded by AF0473. 50 ‫؍‬ 24 M). This is the first Ag ؉ /Cu ؉ -ATPase expressed and purified in a functional form. Thus, it provides a model for structurefunctional studies of these transporters. Moreover, its characterization will also contribute to an understanding of thermophilic ion transporters.

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Section: Resultsmentioning

confidence: 99%

Characterization of a Thermophilic P-type Ag+/Cu+-ATPase from the ExtremophileArchaeoglobus fulgidus

Mandal

Cheung²,

Argüello

2002

Journal of Biological Chemistry

123

192

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“… † The first column shows the 4‐letter abbreviation used throughout the article; the second column contains the full Latin names of the organisms. The literature references for the genomes are the following: Aaeo,70 Aful,71 Bbur,72 Bsub,73 Cpne,74 Ctra,75 Cele,76 Ecol,77 Hinf,78 Hpyl,79 Mgen,80 Mja,81 Mpne,82 Mthe,83 Mtub,84 Phor,85 Rpro,86 Scer,87 Syne,88 and Tpal 89. The third column contains the total number of ORFs in the genomes, and the fourth shows the number of ORFs that have at least one match with one of the SCOP 1.39 domains.…”

Section: Methodsmentioning

confidence: 99%

Structural genomics analysis: Characteristics of atypical, common, and horizontally transferred folds

et al. 2002

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We conducted a structural genomics analysis of the folds and structural superfamilies in the first 20 completely sequenced genomes by focusing on the patterns of fold usage and trying to identify structural characteristics of typical and atypical folds. We assigned folds to sequences using PSI-blast, run with a systematic protocol to reduce the amount of computational overhead. On average, folds could be assigned to about a fourth of the ORFs in the genomes and about a fifth of the amino acids in the proteomes. More than 80% of all the folds in the SCOP structural classification were identified in one of the 20 organisms, with worm and E. coli having the largest number of distinct folds. Folds are particularly effective at comprehensively measuring levels of gene duplication, because they group together even very remote homologues. Using folds, we find the average level of duplication varies depending on the complexity of the organism, ranging from 2.4 in M. genitalium to 32 for the worm, values significantly higher than those observed based purely on sequence similarity. We rank the common folds in the 20 organisms, finding that the top three are the P-loop NTP hydrolase, the ferrodoxin fold, and the TIM-barrel, and discuss in detail the many factors that affect and bias these rankings. We also identify atypical folds that are "unique" to one of the organisms in our study and compare the characteristics of these folds with the most common ones. We find that common folds tend be more multifunctional and associated with more regular, "symmetrical" structures than the unique ones. In addition, many of the unique folds are associated with proteins involved in cell defense (e.g., toxins). We analyze specific patterns of fold occurrence in the genomes by associating some of them with instances of horizontal transfer and others with gene loss. In particular, we find three possible examples of transfer between archaea and bacteria and six between eukarya and bacteria. We make available our detailed results at http://genecensus.org/20.

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“…The first 90 amino acids of FfdB were similar to numerous ferredoxins, most notably polyferredoxins associated with the non‐F 420 reducing hydrogenase of M. thermoautotrophicum [15], suggesting the likely presence of at least two iron–sulfur centers. FfdB shows also similarities to the β‐subunits of F 420 ‐reducing hydrogenase and F 420 ‐reducing formate dehydrogenase from other methanogens and to a subunit of the F 420 :quionone oxidoreductase from A. fulgidus [16]. FfdC reveals high sequence similarity with a putative gene product from Methanococcus jannaschii of unknown function.…”

Section: Resultsmentioning

confidence: 96%

The F420H2-dehydrogenase from Methanolobus tindarius: cloning of the ffd operon and expression of the genes in Escherichia coli

Westenberg

Braune²,

Ruppert³

et al. 1999

FEMS Microbiology Letters

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The membrane-bound F420H2-dehydrogenase from the methylotrophic methanogen Methanolobus tindarius oxidizes reduced coenzyme F420 and feeds the electrons into an energy-conserving electron transport chain. Based on the N-terminal amino acid sequence of the 40-kDa subunit of F420H2-dehydrogenase the corresponding gene ffdB was detected in chromosomal DNA of M. tindarius. Sequence analysis, primer extension, and RT-PCR experiments indicated that ffdB is part of an operon harboring three additional open reading frames (ffdA, ffdC, ffdD). The corresponding mRNA transcript and transcription start sites were determined. All four genes could be heterologously expressed in Escherichia coli.

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Erratum: The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus

Cited by 37 publications

References 12 publications

Characterization of a Thermophilic P-type Ag+/Cu+-ATPase from the ExtremophileArchaeoglobus fulgidus

Characterization of a Thermophilic P-type Ag+/Cu+-ATPase from the ExtremophileArchaeoglobus fulgidus

Structural genomics analysis: Characteristics of atypical, common, and horizontally transferred folds

The F420H2-dehydrogenase from Methanolobus tindarius: cloning of the ffd operon and expression of the genes in Escherichia coli

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