Open Access Highly Accessed Research article

Selection and evaluation of reference genes for improved interrogation of microbial transcriptomes: case study with the extremophile Acidithiobacillus ferrooxidans

Pamela A Nieto1, Paulo C Covarrubias2, Eugenia Jedlicki1, David S Holmes23 and Raquel Quatrini2*

Author Affiliations

1 ICBM, Universidad de Chile, Santiago, Chile

2 Center for Bioinformatics and Genome Biology, Fundación Ciencia para la Vida, MIFAB, Santiago, Chile

3 Depto. de Ciencias Biologicas, Facultad de Ciencias de la Salud, Universidad Andres Bello, Santiago, Chile

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BMC Molecular Biology 2009, 10:63  doi:10.1186/1471-2199-10-63

Published: 25 June 2009



Normalization is a prerequisite for accurate real time PCR (qPCR) expression analysis and for the validation of microarray profiling data in microbial systems. The choice and use of reference genes that are stably expressed across samples, experimental conditions and designs is a key consideration for the accurate interpretation of gene expression data.


Here, we evaluate a carefully selected set of reference genes derived from previous microarray-based transcriptional profiling experiments performed on Acidithiobacillus ferrooxidans and identify a set of genes with minimal variability under five different experimental conditions that are frequently used in Acidithiobacilli research. Suitability of these and other previously reported reference genes to monitor the expression of four selected target genes from A. ferrooxidans grown with different energy sources was investigated. Utilization of reference genes map, rpoC, alaS and era results in improved interpretation of gene expression profiles in A. ferrooxidans.


This investigation provides a validated set of reference genes for studying A. ferrooxidans gene expression under typical biological conditions and an initial point of departure for exploring new experimental setups in this microorganism and eventually in other closely related Acidithiobacilli. The information could also be of value for future transcriptomic experiments in other bacterial systems.