Abstract
The biomining bacterium Acidithiobacillus ferrooxidans oxidizes sulfide ores and promotes metal solubilization. The efficiency of this process depends on the attachment of cells to surfaces, a process regulated by quorum sensing (QS) cell-to-cell signalling in many Gram-negative bacteria. At. ferrooxidans has a functional QS system and the presence of AHLs enhances its attachment to pyrite. However, direct targets of the QS transcription factor AfeR remain unknown. In this study, a bioinformatic approach was used to infer possible AfeR direct targets based on the particular palindromic features of the AfeR binding site. A set of Hidden Markov Models designed to maintain palindromic regions and vary non-palindromic regions was used to screen for putative binding sites. By annotating the context of each predicted binding site (PBS), we classified them according to their positional coherence relative to other putative genomic structures such as start codons, RNA polymerase promoter elements and intergenic regions. We further used the Multiple EM for Motif Elicitation algorithm (MEME) to further filter out low homology PBSs. In summary, 75 target-genes were identified, 34 of which have a higher confidence level. Among the identified genes, we found afeR itself, zwf, genes encoding glycosyltransferase activities, metallo-beta lactamases, and active transport-related proteins. Glycosyltransferases and Zwf (Glucose 6-phosphate-1-dehydrogenase) might be directly involved in polysaccharide biosynthesis and attachment to minerals by At. ferrooxidans cells during the bioleaching process.
Highlights
Acidithiobacillus ferrooxidans is an acidophilic Gram-negative autotrophic γ-proteobacterium that obtains its energy through the oxidation of ferrous iron and reduced inorganic sulfur compounds.At. ferrooxidans, along with other bacterial, archeal and eukaryotic microorganisms forms structured biofilm communities in metal-rich low pH environments, where chemolithotrophic metabolism is the primary form of energy acquisition [1]
As a step towards identifying the molecular mechanism involved in biofilm formation in At. ferrooxidans, we have used a bioinformatic strategy to identify genes whose expression might be regulated by AfeR, as it has been described for other transcriptional regulators including CepR, a LuxR-family protein [15,16]
Our bioinformatic prediction allowed the identification of several gene functions associated with the presence of upstream putative quorum sensing cis-regulatory elements
Summary
Acidithiobacillus ferrooxidans is an acidophilic Gram-negative autotrophic γ-proteobacterium that obtains its energy through the oxidation of ferrous iron and reduced inorganic sulfur compounds. The afe-box regulatory element located upstream of afeI is an 18–20 bp palindromic sequence with nearly perfect dyad-symmetry. It overlaps the -35 region of a sigma 70 promoter consensus sequence, as it is in many other bacteria. As a step towards identifying the molecular mechanism involved in biofilm formation in At. ferrooxidans, we have used a bioinformatic strategy to identify genes whose expression might be regulated by AfeR, as it has been described for other transcriptional regulators including CepR, a LuxR-family protein [15,16]. Results revealed that at least 75 genes corresponding to 2.6% of the identified ORFs from At. ferrooxidans could be direct targets for AfeR
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