Dibenzothiophene (DBT) biodesulfurisation (BDS) route using a genetically modified organism, Pseudomonas putida CECT 5279, is studied. Tests of BDS with whole cells and with homogenized cells are carried out by taking samples of the cells during growth. The influence of the growth phases in the evolution of the intermediates of the 4S DBT desulfurising route is shown. Conversions of the five key compounds of the 4S route (DBT, DBTO, DBTO2, HBPS and HBP) are measured. DBT conversion values are maximal with cells obtained after 30 h of growth time. HBP conversion values do not coincide with DBT conversion values, the maximum HBP production is obtained with cells grown for 10 h. A greater intermediate DBTO and DBTO2 accumulation in broth is produced with cells obtained at 5 and 10 h of growth time. Nevertheless, the accumulation in broth of HBPS, another intermediate, is considerably lower than that observed with cells obtained at 23, 30 and 45 h of growth time. Also, the concentration of the reducing equivalents (NADH and FMNH2) and flavin-oxido-reductase activity inside the cells is measured. This showed that the concentration of the reducing equivalents and the activity of the HpaC enzyme in the P. putida cytoplasm do not limit BDS rate. The influence of 4S compound transport across cellular membrane is studied by comparison of results obtained by resting cell assays (whole cells) and with homogenized cells assays (disrupted cells). The results show that there is no accumulation of any compound inside the cells, and that the transport rate across the cellular membrane does not limit the overall biodesulfurisation rate. (c) 2005 Elsevier B.V. All rights reserved.