RubisCO gene clusters found in a metagenome microarray from acid mine drainage

Area of Science:

• Microbiology
• Genomics
• Biochemistry

Background:

• Ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) is crucial for carbon dioxide fixation in autotrophic bacteria.
• Using RubisCO as a phylogenetic marker can be unreliable due to horizontal gene transfer.

Purpose of the Study:

• To develop and apply a new method for analyzing RubisCO gene diversity and genomic content in acid mine drainage (AMD).
• To evaluate the reliability of metagenome microarrays for screening RubisCO genes.
• To understand the microbial community structure in AMD environments.

Main Methods:

• Construction of a metagenome microarray with 7,776 large-insertion fosmids.
• Screening fosmids for RubisCO form I large-subunit (cbbL) genes.
• Sequencing of cbbL-containing fosmids and analysis of cbbL and 16S rRNA gene diversity.
• Phylogenetic and genomic organization analyses.

Main Results:

• Identified 46 cbbL-containing fosmids, with six fully sequenced.
• Revealed distinct form IA and IB RubisCO gene clusters in AMD based on phylogenetic and genomic data.
• Observed coexistence of form I and form II RubisCO gene clusters within a single genomic fragment.
• Evidence suggests widespread horizontal transfer of RubisCO genes in AMD.

Conclusions:

• Metagenome microarrays are effective for screening functional genes like cbbL.
• RubisCO gene evolution in AMD is complex, influenced by horizontal gene transfer.
• Organismal phylogeny may not accurately reflect RubisCO gene history in these environments.