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Background  The development of biological processes that replace the existing petrochemical-based industry is one of the biggest challenges in biotechnology.  Aspergillus niger  is one of the main industrial producers of lignocellulolytic enzymes, which are used in the conversion of lignocellulosic feedstocks into fermentable sugars. Both the hydrolytic enzymes responsible for lignocellulose depolymerisation and the molecular mechanisms controlling their expression have been well described, but little is known about the transport systems for sugar uptake in  A. niger . Understanding the transportome of  A. niger  is essential to achieve further improvements at strain and process design level. Therefore, this study aims to identify and classify  A. niger  sugar transporters, using newly developed tools for in silico and in vivo analysis of its membrane-associated proteome.    Results  In the present research work, a hidden Markov model (HMM), that shows a good performance in the identification and segmentation of functionally validated glucose transporters, was constructed. The model (HMM gluT ) was used to analyse the  A. niger  membrane-associated proteome response to high and low glucose concentrations at a low pH. By combining the abundance patterns of the proteins found in the  A. niger  plasmalemma proteome with their HMM gluT  scores, two new putative high-affinity glucose transporters, denoted MstG and MstH, were identified. MstG and MstH were functionally validated and biochemically characterised by heterologous expression in a  S. cerevisiae  glucose transport null mutant. They were shown to be a high-affinity glucose transporter ( K  m  = 0.5 ± 0.04 mM) and a very high-affinity glucose transporter ( K  m  = 0.06 ± 0.005 mM), respectively.    Conclusions  This study, focusing for the first time on the membrane-associated proteome of the industrially relevant organism  A. niger , shows the global response of the transportome to the availability of different glucose concentrations. Analysis of the  A. niger  transportome with the newly developed HMM gluT  showed to be an efficient approach for the identification and classification of new glucose transporters.    Electronic supplementary material  The online version of this article (doi:10.1186/s13068-015-0317-9) contains supplementary material, which is available to authorized users.

Aspergillus niger membrane-associated proteome analysis for the identification of glucose transporters