|70-1||Bioinformatic prediction of gene functions regulated by quorum sensing in Acidithiobacillus ferrooxidans
|Autores:||Alvaro Banderas (UCH - Universidad de Chile - Facultad de Ciencias / ZMBH - Zentrum für Molekulare Biologie der Universität Heidelberg) ; María Camila Morales (UCH - Universidad de Chile - Facultad de Ciencias) ; Catalina Bravo (UCH - Universidad de Chile - Facultad de Ciencias) ; Nicolas Guiliani (UCH - Universidad de Chile - Facultad de Ciencias) |
Quorum sensing (QS) is a bacterial cell-cell communication phenomenon in which specific gene expression is modified by changes in the concentration of self-produced autoinducers in the surrounding environment. The LuxI/LuxR-type quorum sensing system is ubiquitous in Gram-negative bacteria, where the core molecular components of the system are well conserved, but the identity of the directly regulated gene set or “regulon” varies greatly.
The chemolitoautotroph acidophile bacterium Acidithiobacillus ferrooxidans is an important member of the biomining microbial community. It possesses all functional QS components (AfeI signal synthase, AfeR response regulator, multiple autoinducers and the afe-box cis-acting element), however, its regulon is still unknown. Cell-cell communication could potentially influence bioleaching rate by way of biofilm formation or other related mechanisms. Experimental limitations imposed by the lack of an efficient DNA transformation method for this bacterium lead us to utilize bioinformatic tools to predict the QS regulon.
Based on the modular arrangement of the binding-site for AfeR, the afe-box, a set of Hidden Markov Models (HMMs) were constructed and used to screen for putative binding sites (PBSs) in the genomic sequence of At. ferrooxidans ATCC 23270. This model allowed us to initially identify 273 PBSs for AfeR. By clustering and filtering them according to their position relative to a start codon and their vicinity to a sigma 70 predicted promoter, and also by using the Multiple EM for Motif Elicitation (MEME) tool, the number of PBS was reduced to 62. This set of PBSs allowed the identification of 75 target-genes that might be regulated by QS in At. ferrooxidans, 34 of which have a higher confidence level, such as afeR itself, genes coding for proteins with glycosyltransferase activities possibly involved in polysaccharide biosynthesis, metallo-beta lactamases, and active transport-related proteins.
A putative QS regulon has been defined for At. ferrooxidans. The identification of genes that could be involved in polysaccharide biosynthesis suggests its putative role in biofilm formation in this bacterium. To assess this hypothesis, qRT-PCR are currently running. On the other hand, this strategy could potentially be used to infer QS-regulated functions from DNA sequence data alone, specially metagenomic sequences from otherwise unculturable bacteria.
This work was supported by grants Fondecyt 1080441 and 1120295. MCN and CB were supported by scholarships from CONICYT.
Palavras-chave: Acidithiobacillus ferrooxidans, Acid Mine Drainage, Biofilm, Bioleaching, Quorum Sensing