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Science 18 July 2008:
Vol. 321. no. 5887, p. 342
DOI: 10.1126/science.1158766
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Technical Comments

Comment on "A 3-Hydroxypropionate/4-Hydroxybutyrate Autotrophic Carbon Dioxide Assimilation Pathway in Archaea"

Thijs J. G. Ettema* and Siv G. E. Andersson

Department of Molecular Evolution, Evolutionary Biology Centre, Uppsala University, Uppsala, S-752 36 Sweden.


Figure 1 Fig. 1. Phylogenetic relationships of 4HCD protein sequences and a kingdom analysis (9) of proteins encoded by the genes flanking the 4HCD sequences in the GOS scaffolds. The GOS1 and GOS2 clades are dominated by bacterial genes (also see fig. S1), indicating that these 4HCD gene products are unlikely to function in the proposed archaeal 3-hydroxypropionate/4-hydroxybutyrate pathway for CO2 assimilation. As a control, the results for the same BLASTP-search-based method are depicted for 50 random proteins from C. symbiosum and P. pacifica, respectively (excluding self-hits). The phylogenetic tree of the 4HCD proteins is based on the same sequence alignment as in Berg et al. (1, 9). The scale bar represents a difference of 1 substitution per site, and the numbers at the nodes indicate the resampling estimated log-likelihood (RELL) support values. Only RELL values above 0.95 are shown. Major groups that gave a similar overall topology as found by Berg et al. [figure 3 in (1)] have been collapsed and depicted as triangles. [View Larger Version of this Image (29K GIF file)]
 

Figure 2 Fig. 2. Distribution of the 16 enzymes that make up the 3-hydroxypropionate/4-hydroxybutyrate pathway across archaeal genomes (9). Gene presence was inferred from the archaeal cluster of orthologous groups of proteins (12) (in black shading) or BLASTP searches (in gray shading). The patchy distribution pattern across species hints at the existence of variants of the 3-hydroxypropionate pathway for CO2 assimilation (such as in C. symbiosum and N. maritimus) or at enzymes that connect to or operate in other pathways (13). Species abbreviations: Nitma, Nitrosopumilus maritimus; Censy, Cenarchaeum symbiosum; Metse, Metallospaera sedula; Sulso, Sulfolobus solfataricus P2; Pyrae, Pyrobaculum aerophilum; Thete, Thermoproteus tenax; Calma, Caldivirga maquilingensis IC-167; Thepe, Thermofilum pendens Hrk 5; Stama, Staphylothermus marinus F1; Ighos, Ignicoccus hospitalis; Hypbu, Hyperthermus butylicus; Aerpe, Aeropyrum pernix; Arcfu, Archaeoglobus fulgidus. Enzymes:1, acetyl-CoA carboxylase; 2, malonyl-CoA reductase (NADPH); 3, malonate semialdehyde reductase (NADPH); 4, 3-hydroxypropionyl-CoA synthetase (AMP-forming); 5, 3-hydroxypropionyl-CoA dehydratase; 6, acryloyl-CoA reductase (NADPH); 7, propionyl-CoA carboxylase; 8, methylmalonyl-CoA epimerase; 9, methylmalonyl-CoA mutase; 10, succinyl-CoA reductase (NADPH); 11, succinate semialdehyde reductase (NADPH); 12, 4-hydroxybutyryl-CoA synthetase (AMP-forming); 13, 4-hydroxybutyryl-CoA dehydratase; 14, crotonyl-CoA hydratase [(S)-3-hydroxybutyryl-CoA-forming]; 15, (S)-3-hydroxybutyryl-CoA dehydrogenase (NAD+); 16, acetoacetyl-CoA β-ketothiolase. [View Larger Version of this Image (51K GIF file)]
 

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