RubisCO Gene Clusters Found in a Metagenome Microarray from Acid Mine Drainage

Abstract

bThe enzyme responsible for carbon dioxide fixation in the Calvin cycle, ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO), is always detected as a phylogenetic marker to analyze the distribution and activity of autotrophic bacteria. However, such an approach provides no indication as to the significance of genomic content and organization. Horizontal transfers of RubisCO genes occurring in eubacteria and plastids may seriously affect the credibility of this approach. Here, we presented a new method to analyze the diversity and genomic content of RubisCO genes in acid mine drainage (AMD). A metagenome microarray containing 7,776 large-insertion fosmids was constructed to quickly screen genome fragments containing RubisCO form I large-subunit genes (cbbL). Forty-six cbbL-containing fosmids were detected, and six fosmids were fully sequenced. To evaluate the reliability of the metagenome microarray and understand the microbial community in AMD, the diversities of cbbL and the 16S rRNA gene were analyzed. Fosmid sequences revealed that the form I RubisCO gene cluster could be subdivided into form IA and IB RubisCO gene clusters in AMD, because of significant divergences in molecular phylogenetics and conservative genomic organization. Interestingly, the form I RubisCO gene cluster coexisted with the form II RubisCO gene cluster in one fosmid genomic fragment. Phylogenetic analyses revealed that horizontal transfers of RubisCO genes may occur widely in AMD, which makes the evolutionary history of RubisCO difficult to reconcile with organismal phylogeny.

Metabolic diversity and adaptive mechanisms of iron‐ and/or sulfur‐oxidizing autotrophic acidophiles in extremely acidic environments

“…Levic an et al (2008) reported that Acidithiobacillus spp., but not Leptospirillum spp., harbor genes encoding phosphoribulokinase and sedoheptulose-1,7-bisphosphatase (Table 2). Several forms of Rubisco, one of the most important enzymes involved in the first rate-limiting step of CO 2 fixation (Ellis, 1979), have been identified (I-IV) (Tabita et al, 2007;Guo et al, 2013). Form I Rubisco, which is present in most photo-and chemoautotrophic organisms, is reportedly a hexadecamer containing eight large and eight small subunits (L 8 S 8 ), while form II Rubisco comprises only large subunits (L n ).…”

RubisCO selection using the vigorously aerobic and metabolically versatile bacterium Ralstonia eutropha

“…However, considerable progress has been made toward expressing bacterial homologs of the eukaryotic enzymes in tobacco [18,19], which holds promise for introducing artificially evolved bacterial enzymes in higher eukaryotes. This could be facilitated by recent studies in which metagenomic sampling has identified potentially novel RubisCOs from microbial 'dark matter' [20][21][22][23].…”

Characterization of the microbial community composition and the distribution of Fe-metabolizing bacteria in a creek contaminated by acid mine drainage

“…7). These sequences were closely related to uncultured clones isolated from AMD (100 % sequence similarity, accession number: JX297618) (Brofft et al 2002;Guo et al 2013;Mendez et al 2008) and Metallibacterium scheffleri (99 % sequence similarity of 374 bp). M. scheffleri, isolated from acidic biofilms, is able to oxidize Fe(II) and reduce Fe(III) (Ziegler et al 2013).…”