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Background    Burkholderia pseudomallei  is an intracellular bacteria causing Melioidosis, the disease widely disseminates in Southeast Asia and Northern Australia.  B. pseudomallei  has ability to invade various types of host cell and to interfere with host defense mechanisms, such as nitric oxide (NO). Due to the cross-talk among alternative killing mechanisms in host immune response against invading microbes, autophagy is the molecular mechanism belonging to intracellular elimination of eukaryotic cells that has been widely discussed. However, bacterial evasion strategy of  B. pseudomallei  and host-bacterial protein–protein interaction within autophagic machinery remain unknown.    Methods  Here, we demonstrated the protein–protein interaction study between different strains of  B. pseudomallei , including wild type PP844 and  rpoS  mutant, with autophagy-related protein LC3 that has been constructed, using the modified immunoaffinity hydrophobic chromatography based-technique. Liquid chromatography tandem-mass spectrometry (LC–MS/MS) analysis was utilized for identifying the eluted proteins obtained from the established column. In addition, the expression level of gene encoding candidate protein was predicted prior to verification using real-time quantitative reverse transcription PCR assay (RT-qPCR).    Results  LC3 recombinant proteins could be entrapped inside the column before encountering their bacterial interacting partners. Based on affinity interaction, the binding capacity of LC3 with antibody displayed over 50% readily for hydrophobically binding with bacterial proteins. Following protein identification, bacterial ATP-binding cassette (ABC) transporter periplasmic substrate-binding protein (BPSL2203) was identified as a candidate LC3-interacting protein, which was found only in  B. pseudomallei  wild type. Gene expression analysis and bioinformatics of BPSL2203 were validated the proteomic result which are suggesting the role of RpoS-dependent gene regulation.    Conclusions  Remarkably, utilization of the modified immunoaffinity hydrophobic chromatography with LC–MS/MS is a convenient and reliable approach to a study in  B. pseudomallei -LC3 protein–protein interaction.    Electronic supplementary material  The online version of this article (doi:10.1186/s13578-017-0172-4) contains supplementary material, which is available to authorized users.

cell and bioscience

Investigation of host–pathogen interaction between Burkholderia pseudomallei and autophagy-related protein LC3 using hydrophobic chromatography-based technique