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Background  The genes of the non-phosphorylative L-rhamnose catabolic pathway have been identified for several yeast species. In  Schefferomyces stipitis , all L-rhamnose pathway genes are organized in a cluster, which is conserved in  Aspergillus niger , except for the  lra-4  ortholog ( lraD ). The  A. niger  cluster also contains the gene encoding the L-rhamnose responsive transcription factor (RhaR) that has been shown to control the expression of genes involved in L-rhamnose release and catabolism.    Result  In this paper, we confirmed the function of the first three putative L-rhamnose utilisation genes from  A. niger  through gene deletion. We explored the identity of the inducer of the pathway regulator (RhaR) through expression analysis of the deletion mutants grown in transfer experiments to L-rhamnose and L-rhamnonate. Reduced expression of L-rhamnose-induced genes on L-rhamnose in  lraA  and  lraB  deletion strains, but not on L-rhamnonate (the product of LraB), demonstrate that the inducer of the pathway is of L-rhamnonate or a compound downstream of it. Reduced expression of these genes in the  lraC  deletion strain on L-rhamnonate show that it is in fact a downstream product of L-rhamnonate.    Conclusion  This work showed that the inducer of RhaR is beyond L-rhamnonate dehydratase (LraC) and is likely to be the 2-keto-3-L-deoxyrhamnonate.    Electronic supplementary material  The online version of this article (doi: 10.1186/s12866-017-1118-z) contains supplementary material, which is available to authorized users.

In vivo functional analysis of L-rhamnose metabolic pathway in Aspergillus niger: a tool to identify the potential inducer of RhaR