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Open Access Highly Accessed Research article

In silico identification and characterization of the ion transport specificity for P-type ATPases in the Mycobacterium tuberculosis complex

Lorena Novoa-Aponte1, Andrés León-Torres1, Miyer Patiño-Ruiz1, Jenifer Cuesta-Bernal1, Luz-Mary Salazar1, David Landsman2, Leonardo Mariño-Ramírez23* and Carlos-Yesid Soto1

Author Affiliations

1 Chemistry Department, Faculty of Sciences, Universidad Nacional de Colombia, Bogotá, Colombia, Carrera 30 # 45–03, Ciudad Universitaria, Bogotá, Colombia

2 Computational Biology Branch, NCBI, NLM, NIH, Bethesda, USA

3 PanAmerican Bioinformatics Institute, Santa Marta, Magdalena, Colombia

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BMC Structural Biology 2012, 12:25  doi:10.1186/1472-6807-12-25

Published: 3 October 2012

Abstract

Background

P-type ATPases hydrolyze ATP and release energy that is used in the transport of ions against electrochemical gradients across plasma membranes, making these proteins essential for cell viability. Currently, the distribution and function of these ion transporters in mycobacteria are poorly understood.

Results

In this study, probabilistic profiles were constructed based on hidden Markov models to identify and classify P-type ATPases in the Mycobacterium tuberculosis complex (MTBC) according to the type of ion transported across the plasma membrane. Topology, hydrophobicity profiles and conserved motifs were analyzed to correlate amino acid sequences of P-type ATPases and ion transport specificity. Twelve candidate P-type ATPases annotated in the M. tuberculosis H37Rv proteome were identified in all members of the MTBC, and probabilistic profiles classified them into one of the following three groups: heavy metal cation transporters, alkaline and alkaline earth metal cation transporters, and the beta subunit of a prokaryotic potassium pump. Interestingly, counterparts of the non-catalytic beta subunits of Hydrogen/Potassium and Sodium/Potassium P-type ATPases were not found.

Conclusions

The high content of heavy metal transporters found in the MTBC suggests that they could play an important role in the ability of M. tuberculosis to survive inside macrophages, where tubercle bacilli face high levels of toxic metals. Finally, the results obtained in this work provide a starting point for experimental studies that may elucidate the ion specificity of the MTBC P-type ATPases and their role in mycobacterial infections.

Keywords:
Tuberculosis; Mycobacterium tuberculosis complex; P-type ATPases; Ion transport; Conserved motifs