AIMS The aims of this study were to study the effect of cellobiose or cellulose as a carbon source on the differential protein phosphorylation-dephosphorylation of cytoplasmic and membrane-associated proteins from Ruminococcus flavefaciens FD-1. METHODS AND RESULTS SDS-PAGE analysis was used to compare in vitro labelled proteins (32P-ATP) isolated from R. flavefaciens FD-1 grown on either cellobiose or cellulose as the carbon source. Distinctly different protein phosphorylation patterns were detected depending on carbon source and cell fraction. Analysis of the nature of the phosphorylated proteins indicates that phosphorylated proteins from cellobiose grown cultures are phosphorylated on serine residues, whereas phosphorylated proteins from cellulose grown cultures are phosphorylated on threonine residues. CONCLUSIONS The results of this comparative analysis show a shift from serine phosphorylation of proteins to a threonine phosphorylation when R. flavefaciens FD-1 cells are grown on cellulose as opposed to cellobiose. There appears to be a role for these phosphorylation events in sensing the carbon source for growth and regulating co-ordinated metabolism in R. flavefaciens FD-1. SIGNIFICANCE AND IMPACT OF THE STUDY We have demonstrated that there is a protein phosphorylation system in R. flavefaciens FD-1 that may be the primary sensing system for carbon source by R. flavefaciens FD-1 and the further regulation of gene expression related to cellulose degradation.